Ruiz was born in Zacatecas City, Mexico and raised in Coachella, California. His parents were farmworkers. He graduated from Coachella Valley High School at age 17 and went to the University of California, Los Angeles (UCLA) in 1990, graduating magna cum laude before attending Harvard Medical School (HMS). He was the first Latino to receive three graduate degrees from Harvard University: a Doctor of Medicine (M.D.) from HMS, a Master of Public Policy (M.P.P.) from the John F. Kennedy School of Government and a Master of Public Health (M.P.H.) from the Harvard School of Public Health.