Graham came under criticism for comments he made about Islam in the wake of the September 11, 2001 attacks when he referred to Islam as "a very evil and wicked religion." Further criticism came on April 18, 2003, when he preached at a Good Friday service at the Pentagon. Muslims at Pentagon Incensed Over Invitation to Evangelist Rev. Franklin Graham has made anti-Islamic remarks saying "True Islam cannot be practiced in this country," Graham told CNN's Campbell Brown in December. "You can't beat your wife. You cannot murder your children if you think they've committed adultery or something like that, which they do practice in these other countries." On April 22, 2010 after objections from the Military Religious Freedom Foundation and the Muslim group Council on American-Islamic Relations (CAIR), the Pentagon rescinded his invitation from the Christian conservative National Day of Prayer Task Force to speak at a Pentagon National Day of Prayer event. He still attended the National Day of Prayer meeting at the Pentagon, but outside in the parking lot with about a dozen people.
In the August 30, 2010 issue of the Time magazine, "Is America Islamophobic?" Frank Graham reportedly said that Islam "is a religion of hatred. It's a religion of war." Building the cultural center near Ground Zero, he says, means Muslims "will claim now that the World Trade Center property ... is Islamic land."
On August 19, 2010, when asked by CNN correspondent John King if he had doubts that President Barack Obama is a Christian, Graham stated, "I think the president's problem is that he was born a Muslim, his father was a Muslim. The seed of Islam is passed through the father like the seed of Judaism is passed through the mother. He was born a Muslim, his father gave him an Islamic name."
Graham has also been criticized for refusing to participate in 1994 peace negotiations between the Lord's Resistance Army (LRA) and the Sudanese and Ugandan governments.
When Sudanese President Omar Hassan al-Bashir was indicted by the International Criminal Court in March 2009, Graham argued in an op-ed in ''The New York Times'' that Bashir should not be indicted for alleged genocidal acts because the indictment would lead to the collapse of the 2005 peace agreement. [[People for the American Way]], among others, criticized Graham for downplaying Bashir's war in mostly Muslim Darfur because of peace in the mostly Christian south of Sudan and because Bashir has allowed Graham and his Samaritan's Purse latitude in operating in Sudan.