Ezmai Martin was taken to hospital in Guildford after an incident at a flat in Bordon, Hampshire, on 28 June 2015.
She was transferred to St George's Hospital in London, where she died.
Joshua Martin, of Salisbury Close, Alton, appeared before Basingstoke magistrates and was remanded in custody to appear before Winchester Crown Court on Thursday.
Hampshire Police declined to comment on the relationship between Mr Martin and the baby girl.
A 19-year-old man has appeared in court charged with the murder of a seven-week-old girl.