The alleged attack is believed to have taken place in the Annalong area of County Down, where the infant is from.
Police say the baby suffered a number of injuries in the alleged attack, which happened on Saturday, September 29.
The suspect, who appeared at Armagh Magistrates' Court, cannot be named for legal reasons.
He is due to appear at Newry Magistrates' Court on Wednesday next week.
Details of the incident have emerged on Friday, following a court appearance at Armagh Magistrates Court on Tuesday.
The 25-year-old accused, who cannot be identified for legal reasons, has been charged with sexual assault of a child under 13 and grievous bodily harm of that same child.
The defendant made a brief appearance in the dock in order to hear the charges read out to him following the alleged incident on Saturday, September 29.
A detective sergeant, also present before the court, believes he was able to connect the 25-year-old with the charges. No bail application was made by the defendant’s counsel at this stage.
He was remanded into custody at Maghaberry prison and is due to appear before Newry Magistrates’ Court next Wednesday morning, October 10, via videolink.
The accused man’s address has been given in court as Annalong.