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 provisions for sale to soldiers, and introduces her children Eilif, Kattrin, and Schweizerkas ("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 and companions change their insignia from Protestant to Catholic. Swiss Cheese is captured and tortured by the Catholics having hidden the paybox by the river. Mother Courage attempts bribery to free him, planning to pawn the wagon first and redeem it with the regiment money. When Swiss Cheese claims that he has thrown the box in the river, Mother Courage backtracks on the price, 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, the Chaplain tells Mother Courage that the war will still continue, and she is persuaded to pile up stocks. 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 a drunken soldier. Thereafter Mother Courage is again following the Protestant army.
Two peasants try to sell merchandise to her when they hear news of peace with the death of the Swedish king. The Cook appears and causes an argument between Mother Courage and the Chaplain. Mother Courage is off to the market while Eilif enters, dragged in by soldiers. Eilif is executed for killing a peasant while stealing livestock, trying to repeat the same act for which he was praised as hero in wartime, but Mother Courage never hears thereof. When she finds out the war continues, the Cook and Mother Courage move on with the wagon.
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.
When Mother Courage is trading in the Protestant city of Halle, Kattrin is left with a peasant family in the countryside overnight. As Catholic soldiers force the peasants to guide the army to the city for a sneak attack, Kattrin fetches a drum from the cart and beats it, waking the townspeople, but is herself shot. Early in the morning, Mother Courage sings a lullaby to her daughter's corpse, has the peasants bury it, and hitches herself to the cart.