The message was posted early morning, UK time.
Despite the rift between the brothers, the Cambridges decided to make the message to their nephew public via social media.
Prince Charles and Duchess Camilla have also shared a birthday message for their grandchild.
The Prince of Wales and the Duchess of Cornwall shared a sweet black and white portrait of Charles, Harry and Archie, showing the three generations together.
The Queen has also wished her great-grandson a happy day, sharing one of the official photos from the day the Sussexes introduced Archie to the world.
The royal family have not seen Archie in 18 months, since the Sussexes relocated to Canada and then Los Angeles.
Prince Harry recently travelled to the UK alone for the funeral of his grandfather, Prince Philip. Meghan Markle was advised by her doctor to stay in the US, as she is pregnant with the couple's second child.
The couple will reportedly celebrate Archie's second birthday in private at home today.