The Czech title of this opera, Jeji pastorkyna (her stepdaughter) focuses the entire story on the relationship between two women, brought together by chance, who both have to deal with an impossibly difficult situation.
In the village of Veborany, in Moravia the law condemns women to death by stoning for getting pregnant out of wedlock, Jenůfa is terrified to reveal her secret to anyone. The baby’s father, Števa, has agreed to marry her, but her stepmother, the Kostelnička (Sacristan), will not allow her to marry a known drunkard and womanizer. She asks him to change his behavior and gives him a year to do so. A desperate Jenůfa is forced to tell her stepmother about the baby, and in fear of the consequences and the shame it would bring on the family, the Kostelnička hides her away, whilst praying desperately that she will miscarry.
The baby boy is born healthy, and Jenůfa names him Števa after his father. When the year has passed, the Kostelnička asks Števa if he intends to keep his promise to marry Jenůfa. Števa knew about the pregnancy, and has never once asked about the baby. But Števa has lost interest in Jenůfa, and has promised to marry the Miller’s daughter instead. His half-brother, Laca, who has always harbored a desire for Jenůfa, offers to marry her instead. The Kostelnička tells Laca the truth, that Jenůfa has had Števa’s baby. Fearing that he will leave and not marry Jenůfa, the Kostelnička tells him that the baby has died.
Caught up in her own lies, and desperate not to bring dishonor to the family, the Kostelnička takes the baby while Jenůfa is sleeping. She puts him under the ice in the river, believing that she is sending him to God. When Jenůfa wakes, she tells her that she has been asleep for two days and that the baby died. The truth is only revealed on Jenůfa and Laca’s wedding day, when some workers find the body of Jenůfa’s baby in the ice. The Kostelnička reveals what she has done, and begs for Jenůfa’s forgiveness. Jenůfa understands and forgives her before she is led away to be put on trial.