The play is set in the 17th century in Europe during the Thirty Years' War. The Recruiting Officer and Sergeant are introduced, both complaining about the difficulty of recruiting soldiers to the war. Anna Fierling (Mother Courage) enters pulling a cart containing food and liquor sold to soldiers, and introduces Eilif, Kattrin, and Swiss Cheese. The sergeant negotiates a deal with Mother Courage while Eilif is conscripted by the Recruiting Officer.
Two years thereafter, Mother Courage argues with a Protestant General's cook over a capon, and Eilif is congratulated by the General for killing peasants and slaughtering their cattle. Eilif and his mother sing "The Fishwife and the Soldier". Mother Courage scolds her son for endangering himself.
Three years later, Swiss Cheese works as an army paymaster. The camp prostitute, Yvette Pottier, sings "The Fraternization Song". Mother Courage uses this song to warn Kattrin against involving herself with soldiers. Before the Catholic troops arrive, the Cook and Chaplain bring a message from Eilif. Swiss Cheese hides the regiment's paybox from invading soldiers, and Mother Courage & Co. change their insignia from Protestant to Catholic. Swiss Cheese is captured by the Catholics while attempting to return the paybox to his General. Mother Courage attempts barter with the soldiers to free him; but takes too long trying to negotiate, and Swiss Cheese is killed. Fearing to be shot as an accomplice, Mother Courage does not acknowledge his body, and it is discarded.
Later, Mother Courage waits outside the General's tent to register a complaint and sings the "Song of Great Capitulation" to a young soldier anxious to complain of inadequate pay. The song persuades both to withdraw their complaints.
When Catholic General Tilly's funeral approaches, Mother Courage discusses with the Chaplain about whether the war will continue. The Chaplain then suggests to Mother Courage that she marry him, but she rejects his proposal. Mother Courage curses the war because she finds Kattrin disfigured after being raped by the clerk. Thereafter Mother Courage is again following the Protestant army.
Two peasants try to sell merchandise to her when they find out that peace has begun. The Cook appears and creates an argument between Mother Courage and the Chaplain. Mother Courage departs for the town while Eilif enters, dragged in by soldiers. Eilif is executed for killing peasants, but Mother Courage never hears thereof. When the war begins again, the Cook and Mother Courage start their own business.
In the seventeenth year of the war, there is no food and no supplies. The Cook inherits an inn in Utrecht and suggests to Mother Courage that she operate it with him, but refuses to harbour Kattrin. Thereafter Mother Courage and Kattrin pull the wagon by themselves.
The Catholic army attacks the small Protestant town of Halle while Mother Courage is away from town. Kattrin is woken by a search party, fetches a drum from the cart and beats it to waken the townspeople, but is herself shot. Early in the morning, Mother Courage sings to her daughter's corpse, has the peasants bury it, and hitches herself to the cart.