The race took place about a year after two bombs exploded near the finish line, killing three people and injuring more than 260 others.
American Meb Keflezighi won the men's division of this year's race. He is the first American to win the race in 30 years.
Jason Barhorse was one of the 36,000 in the race.
"I was happy to be here. I was happy to come back," he said. "I feel sorry about everything that happened last year, but just the fact that we were able to come back this year and still be running is more joy than anything."
Kenya's Rita Jeptoo won the women's race in a course record time. She defended her title from last year.
Among the runners in the race were survivors of last year's bombings.
Organizers say a million spectators cheered the racers on - double the usual turnout.