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. A canteen woman named Anna Fierling (Mother Courage) enters pulling a cart that she uses to trade with soldiers and make profits from the war. She has three children, Eilif, Kattrin, and Swiss Cheese. The sergeant negotiates a deal with Mother Courage while Eilif is led off by the recruiting officer. One of her children is now gone.
Two years from then, Mother Courage argues with a Protestant General's cook over a capon, or chicken. At the same time, 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 taking risks that could have got him killed and slaps him across the face.
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 about 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. Mother Courage & co. hurriedly switch their insignia from Protestant to Catholic. Swiss Cheese is captured by the Catholics while attempting to return the paybox to his General. Mother Courage deals her cart to get money to try and barter with the soldiers to free her son. She takes too long trying negotiate small amount of money for herself, the Chaplin, and Kattrin to live from and Swiss Cheese is shot dead with 11 bullets. To acknowledge the body could be fatal, so Mother Courage does not acknowledge it and it is thrown into a pit.
Later, Mother Courage waits outside the General's tent in order to register a complaint and sings the "Song of Great Capitulation" to a young soldier waiting for the General as well. The soldier is angry that he has not been paid and also wishes to complain. The song persuades the soldier that complaining would be unwise, and Mother Courage (reaching the same conclusion) decides she also does not want to complain.
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 while collecting more merchandise.
At some point about here Mother Courage is again following the Protestant army.
Two peasants wake Mother Courage up and try to sell merchandise to her while they find out that peace has broken out. 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 his mother never finds out. When the war begins again, the Cook and Mother Courage start their own business.
The seventeenth year of the war marks a point where 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 he refuses to harbour Kattrin. It is a very small inn. Mother Courage will not leave her daughter and they part ways with the Cook. 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, trading. Kattrin is woken up by a search party that is taking peasants as guides. Kattrin fetches a drum from the cart, climbs onto the roof, and beats it in an attempt to awake the townspeople. Though the soldiers shoot Kattrin, she succeeds in waking up the town.
Early in the morning, Mother Courage sings to her daughter's corpse, has the peasants bury her and hitches herself to the cart. The cart rolls lighter now because there are no more children and very little merchandise left.
