Molina was born in Mexico City to Roberto Molina Pasquel and Leonor Henríquez. His father was a lawyer and diplomat who served as an ambassador to Ethiopia, Australia and the Philippines. His mother was a family manager. With considerably different interests than his parents, Mario Molina went on to make one of the biggest discoveries in environmental science.
Mario Molina attended both elementary and primary school in Mexico. However, before even attending high school, Mario Molina had developed a deep interest in chemistry. As a child he converted a bathroom in his home into his own little laboratory, using toy microscopes and chemistry sets. Ester Molina, Mario's aunt, and an already established chemist, nurtured his interests and aided him in completing more complex chemistry experiments. At this time, Mario knew he wanted to pursue a career in chemistry, and at the age of 11, he was sent to a boarding school in Switzerland at Institut auf dem Rosenberg, where he learnt to speak German. Before this, Mario had initially wanted to become a professional violinist, but his love for chemistry triumphed over that interest. At first Mario was disappointed when he arrived at the boarding school in Switzerland due to the fact that most of his classmates did not have the same interest in science as he did.
Molinas early career consisted of research at various academic institutions. Molina went on to earn his bachelors degree in chemical engineering at the National Autonomous University of Mexico (UNAM) in 1965. Following this, Molina studied polymerization kinetics at the Albert Ludwig University of Freiburg, West Germany, for two years. Finally, he was accepted for graduate study at the University of California, Berkeley. After earning his doctorate he made his way to UC Irvine. He then returned to Mexico where he kickstarted the first chemical engineering program at his alma mater. This was only the beginning of his chemistry endeavors.