Hosseini was born in Kabul, Afghanistan, in 1965. In 1970 Hosseini and his family moved to Iran where his father worked for the Embassy of Afghanistan in Tehran. In 1973 Hosseini's family returned to Kabul, and Hosseini's youngest brother was born in July of that year.
In 1976, when Hosseini was 11 years old, Hosseini's father obtained a job in Paris, France, and moved the family there. They were unable to return to Afghanistan because of the Saur Revolution in which the PDPA communist party seized power through a bloody coup in April 1978. Instead, a year after the Soviet invasion of Afghanistan, in 1980 they sought political asylum in the United States and made their residence in San Jose, California.
Hosseini graduated from Independence High School in San Jose in 1984 and enrolled at Santa Clara University, where he earned a bachelor's degree in biology in 1988. The following year, he entered the University of California, San Diego, School of Medicine, where he earned his M.D. in 1993. He completed his residency in internal medicine at Cedars-Sinai Medical Center in Los Angeles in 1996. He practiced medicine for over ten years, until a year and a half after the release of The Kite Runner.