Mohyeldin covered the 2011 Egyptian protests for Al Jazeera English. On January 28, 2011 Ayman broadcast from the Al Jazeera news building in Cairo for several hours straight reporting on the Egyptian protests, as Protesters and Egyptian Police battled for control of the 6th October Bridge. On January 30th, Anis El Fekki of the Egyptian Interior Ministry revoked Al Jazeera's broadcast license and forced the closure of their Cairo bureau; claiming the network was conspiring with opposition groups to overthrow the government. Ayman was one of five Al Jazeera journalists arrested and briefly detained by Egyptian Authorities the following day, after the network refused to cease broadcasting upon the loss of their accreditation. On February 06, 2011 Mohyeldin was again arrested by the Egyptian military upon trying to enter Tahrir square. He was released 9 hours later
From May 2008 until May 2010, Ayman was the only foreign journalist based in the Gaza Strip. During the 2008/2009 War on Gaza, he was one of the only foreign journalists reporting from Gaza. Since joining Al Jazeera in 2006, Ayman has reported from Europe, the U.S. and across the Middle East where he has covered the siege on Gaza, sectarian strife in Lebanon, Palestinian in-fighting and human rights abuse in the Arabian Gulf. In 2007, Ayman's exclusive report during Egypt's referendum on constitutional amendments exposed serious voting irregularities and violations. Ayman was also among the first journalists to report on Gaza's intricate system of tunnels along its border with Egypt. Before joining Al Jazeera in 2006, Ayman worked for American networks. He was based in Baghdad where he covered the immediate aftermath of the US-led invasion of Iraq. While there, he reported on the daily struggle of ordinary Iraqis and embedded with the US military to report on the Iraqi insurgency. Ayman was among the few international journalists allowed to observe and report on the US handover of Saddam Hussein to an Iraqi judge. He has also produced exclusive reports from Libya where he was the first journalist to enter one of Libya's nuclear research facilities. Ayman began his journalism career working for the American network NBC in Washington where he covered the inauguration of US President George Bush, the September 11 attacks and the war in Afghanistan.