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Hernández has earned or been awarded:
Graduate Engineering Minority Fellow (GEM) (1985)
Hispanic Engineer National Achievement Award, "Outstanding Technical Contribution" (1995)
Society of Mexican American Engineers and Scientists (MAES) "Medalla de Oro" recipient for professional and community contributions (1999)
U.S. Department of Energy "Outstanding Performance Commendation" (2000)
NASA Service Awards (2002, 2003)
Lawrence Livermore National Laboratory "Outstanding Engineer Award" (2001)
Upward Bound National TRIO Achiever Award (2001)
Eta Kappa Nu Electrical Engineering Honor Society member and awarded an honorary LL.D. degree from University of California at Santa Barbara (2006).
José Hernández Middle School, in San Jose, California, is named after him[14]
University of California, Santa Barbara 2015 Distinguished Alumnus[11]
United States Hispanic Leadership Institute, 2016 National Hispanic Hero Award
University of the Pacific 2019 Medallion of Excellence for outstanding and exceptional service to University of the Pacific, their profession and community.