The child was admitted to Chon Buri Hospital on Jan 16 after he convulsed and collapsed after eating a chili given to him by the babysitter. He died three days later.
The exact cause of death was not given but doctors said the boy had suffered from swelling on the brain. There were many bruises on his body and a chili was found in his stomach.
The arrest came after the boy's mother, Maeree Nammontri, 36, sought help from the Pavena Foundation for Children and Women, Thai media reported. Pavena Hongsakula, who chairs the foundation, took her to file a complaint with Chon Buri police on Thursday.
Police later took Ms Wanwisa in for questioning. Initially she insisted she had not assaulted the boy. However, after intensive interrogation she admitted to having pushed Nong Garfield, causing his head to hit a concrete wall before he fell to the ground on Jan 15.
She claimed she had asked the boy to follow her to the bathroom so she could change his soiled diaper, but he was walking too slowly.
Later on the same day, she told police, the boy climbed over a door railing and fell to the ground.
She said she had bought fresh chilies and gave one to the boy. He ate a chili and shortly afterward she noticed tears in his eyes although he was not crying. He then went into convulsions and collapsed and she took him to the hospital.
Police said the woman insisted she had no intention to harm the boy.
Pol Maj Gen Amphon Buarapporn, chief of the Chon Buri police, said offivers were not convinced by the woman's account of events. Consequently, investigators have pressed charges of assault causing death.