The woman, identified as Katharina Katit-Staheli, 40, lost custody of her son, Dylan, in December after she refused to take him to a hospital to receive urgent medical care for a birth defect, TheLocal.es reported.
Katit-Staheli then illegally took Dylan on Christmas Day.
The two were found in Torrevieja, Spain several days ago, local media reported. Both were in good health, but taken to a local hospital for medical attention and Katit-Staheli was placed under arrest.
It was unclear how Katit-Staheli obtained a knife or whether the two were in a room alone together when she allegedly stabbed the baby to death Wednesday.
No other details were reported.