He has visited mosques in other parts of the world on official trips abroad during his seven years as president. The White House said the visit was intended as a defence of religious freedom and a statement against bigotry.
`Tradition of religious freedom`
The president would "reiterate the importance of staying true to our core values - welcoming our fellow Americans, speaking out against bigotry, rejecting indifference, and protecting our nation`s tradition of religious freedom," a White House official was quoted by Reuters as saying.
Advocacy group Council on American-Islamic Relations (CAIR) says it has tracked a growing number of attacks on mosques and Muslim individuals since the Paris attacks in November 2015 and a shooting in San Bernardino, California, in December.
A report by the group warned that "levels of anti-Muslim sentiment follow trends in domestic US politics", highlighting Republican presidential candidate Donald Trump`s call in December for a temporary ban on Muslims entering the US.
Ibrahim Hooper from CAIR said: "I don`t think there`s ever been this level of fear and apprehension in the Muslim-American community.
"For some time, we`ve been asking for pushback. Perhaps this will start a trend."
Mr Obama is in his final year as president. A week ago, he became the first sitting president to speak at the Israeli Embassy, where he warned of growing anti-Semitism.
Akbar Ahmed, an Islamic studies specialist at American University, said Mr Obama had left it "literally to the last" to visit a US mosque, but he said: "Better late than never."
In 2010 the White House blamed a "misinformation campaign" for a growing belief that Mr Obama was a Muslim. Over the course of his presidency, some people have said he is a Muslim pretending to be a Christian.
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