Katharina Katit-Stäheli stabbed her son to death in a hospital in the Spanish coastal town of Torrevieja, local media reported on Thursday.
She then tried to kill herself by slashing her own throat, and required immediate surgery at the same hospital.
The 40-year-old had found herself in the hospital after being detained by police at Torrevieja's Carrefour shopping centre.
Her arrest came just days after authorities from the canton of Zurich called on Spanish police to help find the woman and her son Dylan.
Dylan had serious birth defects but Katit-Stäheli lost custody of him in December after refusing to take him to hospital for urgent medical treatment.
Katit-Stäheli then illegally took her son from the Zurich children's hospital and the pair had been missing since Christmas.
On the Swiss woman's arrest, Dylan was found to be healthy but the two were taken to a hospital in Torrevieja so that the boy could receive medical attention.
Spanish authorities had intended to send the pair back to Switzerland.
It is not known how the boy's mother obtained the knife or whether the two were alone in a hospital room when the alleged murder occurred.
Katit-Stäheli was described as a staunch vegan and horse lover by Spanish local daily La Verdad.
The paper also reported the woman has an adult daughter from a previous marriage, and that Katit-Stäheli has no contact with Dylan's father.