Molina, the son of a diplomat, studied chemical engineering at the University of Mexico. After further study in Europe at the University of Freiburg and at the Sorbonne, Molina moved to the University of California, Berkeley, where he gained his PhD in 1972. He worked initially as a postdoctoral student at the Irvine campus of the University of California with F. S. Rowland. Following a spell at the Jet Propulsion Laboratory he moved to MIT in 1989 as professor of environmental sciences.

Rowland had become interested in the fate of the chlorofluorocarbons (CFCs) used as the propellant in most aerosol cans, and asked his new colleague if he would be interested in working out what happened to them as they rose into the stratosphere. It would be, Molina later confessed, “a nice, interesting, academic exercise.”

He quickly worked out that as CFCs were stable they would eventually accumulate in the upper atmosphere. There, he argued, they would be broken up by ultraviolet light and chlorine atoms would be released. Rowland suggested that Molina should analyze how free chlorine atoms would behave. Molina suspected that a chain reaction would be produced, reducing the amount of ozone in the upper atmosphere. Despite this, Molina still thought the effect would be negligible. It was only when he discovered that the amount of CFCs released each year was about 1 million tonnes that he realized that much of the ozone layer could be destroyed. Molina published his results in a joint paper with Rowland in 1974. The National Academy of Sciences issued a report in 1976 confirming the work of Molina and Rowland and in 1978 CFCs used in aerosols were banned in the United States. In 1984 Joe Farman detected a 40% ozone loss over Antarctica.

For his work on CFCs and the ozone layer Molina shared the 1995 Nobel Prize for chemistry with Rowland and Paul Crutzen, thus becoming the first Mexican to receive a Nobel Prize for science.