The novel opens with all of the main characters traveling by train or car to a ferry that will take them to a mysterious island named Indian Island. Each guest has received an invitation from a Mr. or Mrs. U.N. Owen, or a Mrs. Constance Culmington, to come to the island. Vera Claythorne is going because Mrs. U.N. Owen has offered her a secretarial job. Phillip Lombard is going because he has been offered a hundred guineas to go. Miss Emily Brent received her invitation from someone she thinks she remembers on a previous holiday. General Macarthur goes on the pretense that he will be meeting up with some old military friends. Dr. Armstrong is on his way because he was summoned to care for a few elderly women with lots of money. Mr. Blore has been sent to spy on the other guests; he is a former detective. Finally, Anthony Marston recklessly drives his sports car towards the house with the belief that there will be a fabulous party with rich and famous people.
As they travel towards the island, each has a brief moment of remembering a traumatic experience from their past. Each, it seems, has been involved in some way with a past death. For some, they are clearly related to the deaths. For others, the connection is less sure. The guests arrive at the ferry. The captain, Fred Narracott, thinks that this is a strange crew and not the young rich crowd he had been expecting. When they arrive at the island, Mr. and Mrs. Rogers, the house’s servants, escort them to their rooms. The characters learn that they have not actually met Mr. and Mrs. U.N. Owen; the servants had only been hired a few weeks before. In her room, Vera Claythorne discovers an old piece of parchment in her room. On it is the rhyme of the Ten Little Indian Boys. The rhyme chronicles the actions and deaths of ten Indian boys. Each are killed until there were none.
At dinner, the guests begin to acquaint themselves with one another and become more comfortable with their surroundings. Later, in the drawing room, all sit listening to the sound of the ocean when, suddenly, a booming voice echoes through the room. The voice charges the guests with a list of indictments. Each guest is named and then implicated in the murder of a person. When the voice ends, there is a scream and the sound of someone falling. Mrs. Rogers had fainted upon hearing the voice read her name. In the next room, the guests find a gramophone with a record on it. When they play the record, they again hear the voice. Mr. Rogers had been the one to play the record, but he swears he had only done in on the instructions of Mr. Owen. Each guest then gives their story of how they were invited to the island. Mr. Justice Wargrave notes that the initials of their host, U.N. Owen, is a puzzle--it stands for "UNKNOWN!" The judge tells them that a homicidal lunatic may have called them to the island.
The group then begins to explain the circumstances behind the acts of murder for which they are accused. Each guest has a reasonable explanation, though it is obvious some are wracked with guilt over the incidence. Only Anthony Marston and Phillip Lombard seem to show no remorse over the deaths they caused. Rogers tells the group that it will be morning before the boat returns with supplies for the island. As he says this, Anthony Marston takes a sip of his fresh drink and starts to choke. He falls to the floor and dies. All of the guests surmise that it must be suicide, although this seems as unlikely as someone having the opportunity to put poison in his drink. As all the guests then go to bed, Rogers goes into the dining room and is puzzled to find that one statue off a ring of Ten Little Indian statuettes is missing.
Through scenes of internal dialogue, the reader learns of the motivations behind some of the deaths each guest is accused of causing. General Macarthur, for instance, sent his wife's lover into battle knowing that he would be killed. Vera Claythorne recalls the day that she told Cyril, the child she had been caring for, that he could swim out to a rock in the ocean. Cyril drowned. Armstrong has a vivid dream in which he stands over the body of the woman he is accused of murdering. He performed an operation on her while intoxicated. Armstrong is awakened by Rogers, who tells him that his wife will not wake up. Armstrong checks on her to find that she is dead, likely poisoned by a lethal dose of sleeping medicine. After breakfast that morning, General Macarthur begins to have the strange feeling that they will never leave the island. In the house, Rogers discovers that another Indian china figure is missing and he is frightened.
Miss Brent and Vera Claythorne discuss the accusations of murder; Miss Brent is sure that the Rogers are guilty of killing their charge. Miss Brent explains that the girl she is accused of murdering was an immoral girl who became pregnant while working for her. Miss Brent kicked her out of her house and the girl eventually committed suicide. Lombard and Armstrong discuss the situation on the island and Lombard suggests that they have all been called here to account for crimes that they cannot be tried for. They enlist Blore for help and begin searching the island for hiding places and secret passages, but they find nothing.
The guests begin to accuse each other of conspiring in the crimes. Lombard is questioned on why he brought a pistol to the island, and Blore insinuates that perhaps Armstrong put a poison in Mrs. Rogers brandy. At lunch, the guests notice that a storm is coming soon to the island. Armstrong goes to call in General Macarthur to lunch and discovers that he has been killed by a blunt trauma to the head. As they bring the General's body into the house, the storm breaks and the island is cut off from the mainland. When they return to their meal, the notice that only seven Indian figurines remain.
Using reason and logic, Judge Wargrave leads all the guests in a process of deduction over who the killer must be. No one, the judge proclaims, can be excluded "on the score of character, position, or probability." It each person on the island had the opportunity to cause each of the deaths. No one except the dead can be excluded.
Later, all of the guests sit and discuss who they believe might be the murderer. Each has a different theory, mostly based on the character of each guest. During tea, Rogers discovers that a bathroom curtain has gone missing, a curious small incident that still induces fear. After dinner, all of the guests bolt their doors tight, afraid of what might happen during the night. Rogers locks the door to the dining room so that the murderer will have no opportunity to break another of the Indians.
In the morning, they awake late to discover that Rogers has not woken them up. In the unlocked dining room, they discover that another of the Indian figures has been broken. They go looking for him and find Miss Brent already wandering the property in her rain gear. They soon discover Rogers, dead, in the woodshed. He had been given a fatal blow to the head while chopping wood. Vera begins to go a little crazy, asking if there is a beehive on the island since the next verse of the rhyme says that an Indian boy was killed by being stung by bees.
After breakfast, everyone except Miss Brent goes into the kitchen to clean up. Miss Brent suddenly begins to feel drowsy and soon feels a pin prick, like a bee sting, in her neck. Soon, the guests discover Miss Brent's body in the dining room. She is dead from a dose of cyanide administered by hypodermic needle. There is a bee in the room. Armstrong admits that he brought a needle with him as he always does. When they go to his room, they find the needle missing. Each guest then submits to a search of his person. Judge Wargrave takes all the guests’ medicine and locks it away so that no one has access to it. They discover that Lombard's revolver is missing and search the house for it, but they do not find it.
The remaining guests are now more like animals than humans. They are each suspicious of each other. Vera decides she cannot sit in the drawing room with them anymore and goes to her room to take a bath. When she enters the room, she is overcome by the smell of the sea. It smells exactly like the day that Cyril drowned. She feels something grabbing a hold of her neck. She screams and the men run up to her room. They think that they have just avoided the next murder. When they return to the drawing room, however, they discover Mr. Justice Wargrave, outfitted with the bathroom curtain and Miss Brent's ball of wool on his head made to look like a sitting judge. Armstrong removes the wig and discovers a gunshot wound to his head. When they all go to bed that evening, Lombard is surprised to find his revolver returned to the drawer in his bedside table. In her room, Vera notices for the first time a big black hook hanging from the ceiling.
Early the next morning, Blore awakens to hear footsteps down the hall. He immediately goes to the other rooms, knowing that the killer must be the person not in their room. Vera and Lombard both answer their doors but Armstrong does not. Lombard and Blore begin to search the island but return to tell Vera that Armstrong has disappeared and that another of the Indian figurines has been smashed.
The storm passes and the group tries to think of ways to leave the island. They are out on a cliff, flashing S.O.S. signals when Blore leaves to go back into the house. Vera and Lombard hear a crash and go to the house to find Blore lying dead on the ground. He had been hit over the head with a marble clock shaped like a bear, thereby fulfilling a verse of the rhyme. They both now believe that the killer must be Armstrong. They go back to the cliffs, and Vera sees a pile of clothes lying on the beach. They go and discover that it is Armstrong's body. He has been drowned in the ocean. Vera, knowing the killer is Lombard, picks his pocket of the revolver. As Lombard leaps for the weapon, Vera shoots him in the heart, killing him. In a state of shock, Vera walks back to her room. She begins to have visions of her lost love, Hugo, and remembers the day that Cyril drowned. She finds a noose hanging from the hook in her bedroom. She steps onto a chair and hangs herself.
Sometime later, two detectives at Scotland Yard sit and discuss the curious case of the murders on Indian Island. They go over the facts of the case, the order in which each is killed, and the method by which they met their deaths. It seems that Vera Claythorne would be the murderer since Armstrong's body had obviously been laid out on the beach and because Lombard had been shot with Vera's prints on the revolver. However, the chair that Vera had stood on to hang herself had been moved after her death, meaning that someone was on the island after all the murders had been committed. The people on the mainland, however, are sure that no one could have left the island because of the storm. The police are exasperated over the case.
The final chapter of the novel is a confession letter signed by the killer. The killer explains his motivations and means for killing the guests. He tells them that he had always had a keen sense of justice and that he had wanted his act of murder to be a grand piece of art. He had killed the guests in order of their guilt, following the nursery rhyme as best possible. The killer tells them that the judge's murder had been a ruse; Armstrong had helped him fake his own death so that he could then spy on the other guests and determine who the killer really was. It was with great pleasure that the killer watched as the guests descended into psychological barbarism before Vera Claythorne eventually took her own life. The killer then set up a method to kill himself with a gunshot to the head. He had written this confession first, stuffed it in a bottle, and thrown it out to sea. The letter is signed by Lawrence Wargrave.