Emergency services were called to a home in Bidwill, around 20 minutes from Penrith, following reports the baby was unresponsive.
Police confirmed that the post-mortem examination revealed that the child died as a result of a significant brain injury.
The 24-year-old man was arrested at Mount Druitt Police Station just two days later.
The father was due to face Mount Druitt Court today but did not appear and did not apply for bail.
The matter is due to return to court in February next year.