"In some areas of the Middle East where church bells have rung for centuries on Christmas Day, this year they will be silent," Obama said in a statement released by the White House.
"This silence bears tragic witness to the brutal atrocities committed against these communities by ISIL," he said, referring to the acronym used for the Islamic State which controls territories in Syria and Iraq.
Obama has been criticized by Republicans in Congress and on the presidential campaign trail for being too soft on refugees who are fleeing the Islamic State, the majority of whom are Muslim.
Republican presidential candidate Senator Ted Cruz has proposed allowing only Christian refugees into the United States, a suggestion the White House has derided.
Cruz has argued that Christian refugees do not threaten U.S. national security in the same way the Muslims do.
As the Obamas prepare to celebrate Christmas on Friday in Hawaii, the president said in the statement that he and his wife Michelle are "ever-mindful" that "many of our fellow Christians do not enjoy do not enjoy that right" to celebrate openly.
Obama said they "hold especially close to our hearts and minds those who have been driven from their ancient homelands by unspeakable violence and persecution."
He quoted a Christmas carol: "The Wrong shall fail, The Right prevail, With peace on earth, good-will to men."