Molina is the son of Roberto Molina-Pasquel, a Lawyer and judge who went on to serve as chief Ambassador to Ethiopia, Australia and the Philippines in 1923, and Leonor Henríquez. As a child he converted a bathroom into his own little laboratory, using toy microscopes and chemistry sets. He also looked up to his aunt Esther Molina, who was a Chemist, and who helped him with his experiments.

After completing his basic studies in Mexico City and at the Institut auf dem Rosenberg in Switzerland he earned a bachelor's degree in chemical engineering at the National Autonomous University of Mexico (UNAM) in 1965. Two years later he earned his postgraduate degree at the Albert Ludwigs University of Freiburg, West Germany, and a Ph.D. in chemistry at the University of California, Berkeley in 1972. Molina married Chemist Luisa Y. Tan in July 1973. They moved to Irvine, California that fall.

Mario Molina joined the lab of Professor F. Sherwood Rowland in 1973 as a postdoctoral fellow. Here, Molina continued Rowland's pioneering research into "hot atom" chemistry, which is the study of chemical properties of atoms with, and only with, excess translational Energy owing to radioactive processes. This study soon led to research into chlorofluorocarbons (CFCs), which had been accumulating in the atmosphere. Rowland and Molina had investigated other compounds similar to CFCs before, and together they developed the CFC ozone depletion theory. Molina tried to figure out how CFCs might be destroyed in the lower atmosphere, but nothing seemed to work. He and Rowland knew that if CFCs released into the atmosphere do not decay by other processes, they continually rise to higher altitudes until they are destroyed by solar radiation. They discovered that chlorine atoms, produced by the decomposition of CFCs, catalytically destroy ozone. Rowland and Molina published their findings in Nature on June 28, 1974, and also made an effort to announce their findings outside of the scientific community, informing policy makers and the news media of their work. Attesting to the continuing importance of their discovery, to this day there are still laws that protect the ozone layer by regulating the use of CFCs.

He also won the 1987 Esselen Award of the Northeast section of the American Chemical Society,

In 1988 he won the Newcomb-Cleveland from the American Association for the Advancement of Science.

A few other awards he won were the 1989 NASA Medal for Exceptional Scientific Advancement and the 1989 United Nations Environmental Programme Global 500 Award.

In 1990, the Pew Charitable Trusts Scholars Program in Conservation and the Environment honored him as one of the ten environmental Scientists and awarded him a 150,000 dollar grant.

Mario Molina received several awards and honors, sharing the 1995 Nobel Prize in chemistry with Paul J. Crutzen and F. Sherwood Rowland for their discovery of the role of CFCs in ozone depletion.

He received the 1998 Willard Gibbs Award from the Chicago Section of the American Chemical Society and the 1998 American Chemical Society Prize for Creative Advances in Environment Technology and Science

Molina is a member of the Pontifical Academy of Science, the National Academy of Sciences, the Institute of Medicine and The National College of Mexico. He serves on the boards of several environmental organizations and also sits on a number of scientific committees including the U.S. President's Committee of Advisors in Science and Technology, the Institutional Policy Committee, the Committee on Global Security and Sustainability of the John D. and Catherine T. MacArthur Foundation and the Mario Molina Center. He also served on the board of trustees for Science Service, now known as Society for Science & the Public, from 1999-2006. He has also received more than thirty honorary degrees and Asteroid 9680 Molina is named in his honor. In 2003 he was one of twenty-two Nobel Laureates who signed the Humanist Manifesto.

Between 1974 and 2004 he variously held research and teaching posts at University of California, Irvine, the Jet Propulsion Laboratory at Caltech and the Massachusetts Institute of Technology (MIT), where he held a joint appointment in the Department of Earth Atmospheric and Planetary Sciences and the Department of Chemistry. On July 1, 2004 Molina joined the Department of Chemistry and Biochemistry at University of California, San Diego and the Center for Atmospheric Sciences at the Scripps Institution of Oceanography.

Molina and his first wife, Luisa Tan Molina, divorced, and he married his second wife, Guadalupe Álvarez, in February 2006. His only son works as a physician in Boston. Molina was named by U.S. President Barack Obama to form a transition team on environmental issues.

On August 8, 2013, President Barack Obama announced Molina as a recipient of the Presidential Medal of Freedom citing in the press release: