The incident happened at about 5.10pm on Tuesday in the village of Crossgates.
The boy died at the scene and police are investigating the circumstances.
A Police Scotland spokesman said: “Police in Fife are investigating after a child was killed during a collision on a farm in Fife.
“The incident happened around 5.10pm on Tuesday February 14 at a property in Crossgates.
“A three-year-old boy sustained fatal injuries after he was involved in a collision with a farm vehicle and was pronounced dead at the scene.
“Inquiries into the full circumstances surrounding this matter are continuing.”