Soon after the 1993 attack the FBI, on April 21, 1993, made him the 436th person to be added to the Ten Most Wanted Fugitives list.
Inter-Services Intelligence (ISI) and U.S. Diplomatic Security Service Special Agents, including Bill Miller and Jeff Riner, captured Yousef in Islamabad, Pakistan. On February 7, 1995, they raided room number 16 in the Su-Casa Guest House in Islamabad and captured Yousef before he could move to Peshawar.[13] He was captured from a tip-off by Istaique Parker a man that Yousef had tried to recruit. Parker was paid $2 million for the information leading to Yousef's capture (Rewards for Justice - RFJ).[3][4] During the raid agents found Delta Air Lines and United Airlines flight schedules and bomb components in children's toys,[17] and Yousef was found to have chemical burns on his fingers.
Yousef was sent to a prison in New York City and held there until his trial. In court Yousef said, "Yes, I am a terrorist, and proud of it as long as it is against the U.S. government and against Israel, because you are more than terrorists; you are the one who invented terrorism and using it every day. You are butchers, liars and hypocrites."[7] On September 5, 1996, Yousef and two co-conspirators were convicted for their role in the Bojinka plot and were sentenced to life in prison without parole. U.S. District Court Judge Kevin Duffy referred to Yousef as "an apostle of evil" before recommending that the entire sentence be served in solitary confinement.[20]
On November 12, 1997 Yousef was found guilty of masterminding the 1993 bombing and in 1998 he was convicted of "seditious conspiracy" to bomb the World Trade Center towers.[21][22]
The judge sentenced Yousef to 240 years for the Trade Center attack, and life in prison for killing Haruki Ikegami in 1994.