The award in the category of companies with 500 to 1,999 employees was announced by the San Francisco Business Times and the Silicon Valley/San Jose Business Journal.
The publications said the airport's wellness program "has taken off" after years of flying under the radar.
They cited the facility's creation of a Wellness Advisory Council and a series of programs aimed at helping workers achieve healthy physical, emotional, spiritual and financial lifestyles.
One program this year was a 10-week walking challenge.
Airport spokesman Michael McCarron said 628 workers, divided into 30 teams, participated in the challenge. The employees were given pedometers to measure their progress in the goal of walking 1,016 miles during the 10 weeks. McCarron said 27 teams met the goal.
Other projects included stretch breaks, organic gardens, monthly safety meetings, yoga classes, free flu shots and a quarterly health and wellness newsletter.
Airport Director John Martin said, "San Francisco International Airport is extremely honored to be recognized" for its programs.
"The airport's most vital resource is its employees," Martin said.