Kevin Park, from Kelty, made no plea or declaration at Dunfermline Sheriff Court and was remanded in custody.
Police were called to a house in Croftangry Road in the town on Sunday evening. Madison was taken to the Victoria Hospital in Kirkcaldy, where she was pronounced dead.
Her family said she was a "beautiful little girl with a smile for everyone".
Mr Park is due to appear in court again on 30 April.
In a statement issued through Police Scotland, Madison's family said the two-year-old had had "a happy life ahead of her".
They added: "She was a much loved daughter who will be sorely missed by all who knew her. We would ask that our privacy be respected at this time to allow us to grieve."
Forensic officers carried out investigations at the scene