He is due to deliver the university's commencement address, a speech given to graduating students, later on Thursday. After receiving the honour he posted a photo of him with his parents Edward and Karen Zuckerberg.
Zuckerberg returned to the room where he built Facebook along with his co-founders, Dustin Moskovitz, Eduardo Saverin, Andrew McCollum and Chris Hughes.
On Wednesday, he said his upcoming speech would "share what I've learned about our generation and the world we're all building together".
Even after the company moved its headquarters to California, Zuckerberg continued to be enrolled at Harvard until he dropped out in November 2005. "I'm not coming back" he told the university paper The Crimson.
His honorary degree comes 12 years later, a little quicker than it took Bill Gates, another famous Harvard dropout to get his. Gates, who left to found Microsoft in 1975, did not receive his honorary degree until 2007.
Last week, Zuckerberg shared a video of him finding out he had been accepted into Harvard.
Moment a teenage Mark Zuckerberg finds out he got into Harvard