The Family Guy creator will become the only three-time host of the series, after previously taking the helm for David Hasselhoff and Donald Trump's roastings.
Comedy Central Roast of Charlie Sheen will be recorded on Saturday, September 10 in Los Angeles. It will premiere on Monday, September 19 at 10pm ET/PT.
"I'm very excited to work with Comedy Central again on the roast," said MacFarlane. "Charlie is a true icon with a talent that is strong and pure and concentrated into small crystals which can be smoked or eaten."
Comedy Central's head of programming Kent Alterman added: "In addition to his sharp wit, Seth is way more suave and sophisticated than we are. We continue to try and soil him."
Charlie Sheen's roast is purposely scheduled on the same evening as his former sitcom Two and a Half Men's premiere episode with new star Ashton Kutcher.
The actor recently denied reports that he will be a housemate in the upcoming series of UK Celebrity Big Brother on Channel 5.