In Afghanistan, Rutskoy served as the commander of an independent air attack regiment of 40th Army. During the war, his aircraft was shot down twice, but on both occasions he managed to eject safely. On one of these two occasions, his Su-25 aircraft entered Pakistani airspace, and suffered multiple strikes, forcing Rutskoy to eject. Rutskoy ejected safely, but was captured by local people and was briefly held as a POW in Islamabad, Pakistan. The U.S. Central Intelligence Agency intervened to save him to avoid interfering with the Geneva Accords and the Soviet withdrawal from Afghanistan. For his bravery and having flown 428 combat missions, he was awarded the title of Hero of the Soviet Union in 1988. He was chosen by Boris Yeltsin to be his vice-presidential running mate in the 1991 Russian presidential election.