The social networking site will also host a livestream from the White House, featuring tips from Facebook, MTV and White House staff about how to prevent bullying online.
Viewers will also be able to pose questions to the panel on a dedicated Facebook page. The live stream will air in the UK at 5.20pm today.
In the video message President Obama says: “For a long time, bullying was treated as an unavoidable part of growing up but more and more we’re seeing how harmful it can be for our kids, especially when it follows them from their school, their phone [and] their computer screen.”
Facebook has come under pressure from campaigners to ensure it is safe for children following reports of cyber bullying on the site.
Facebook says: “Building a trusted environment is fundamental to our mission and to ensure a positive experience for people who use our site.”
The company adds it takes steps to reduce the likelihood of online bullying on the site and has tried to reduce and diminish its impact should an incident occur.
Facebook has a dedicated “Safety Centre” with information about how users can stay secure.
The Obama video message will push an anti-bullying conference taking place at the White House tomorrow (10 March).