The charge relates to a cartoon published in 2007 that used the name Mohammed, a common first name in Bangladesh, and an article published in 2013 that prosecutors say misinterpreted a verse of the Quran.
Mr MatiurRahman, who edits the daily Prothom Alo, was accused of hurting religious sentiment in a case filed last October.
Prothom Alo is Bangladesh's most widely read newspaper with a circulation of around half a million and has a reputation for being politically neutral.
Public prosecutor Alam Khan Kamal told AFP the judge had issued the arrest warrant after Mr Rahman failed to appear in court on three consecutive occasions.
Mr Rahman did not immediately answer calls for comment.
Activists have accused the Bangladesh government of seeking to muzzle its critics, and the warrant came weeks after authorities forced off air a private television station that broadcast a speech by the son of the opposition leader.
It comes at a politically sensitive time for Bangladesh, where opposition protests have killed 29 people in recent weeks.
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