The White House suggested earlier this month that this was going to happen, but now we have official confirmation (via CBS News):
President Obama in March will travel to Vatican City to meet with Pope Francis, the White House announced Tuesday. Mr. Obama looks forward to discussing with the pope their “shared commitment to fighting poverty and growing inequality,” White House press secretary Jay Carney said in a statement.
The March 27 stop will be Mr. Obama’s second visit to the Vatican -- on July 10, 2009, he met with Pope Benedict XVI. During that meeting, Mr. Obama and the pope discussed a range of topics including abortion, embryonic stem cell research, Middle East peace and aid to Africa. Every U.S. president since Eisenhower has traveled to the Vatican to meet with the pope.
Obama has had kind words for Francis in recent months, perhaps most notably quoting the pope's remarks during a speech on income inequality last month.