While at SWJC, Thompson completed a master's degree at the University of Oklahoma. While working on a doctorate at the University of Chicago, he was asked to head the physics and mathematics department at Emmanuel Missionary College, now Andrews University.

Following completion of his doctorate, Thompson became chair of the physics department at La Sierra College, now University, in 1946, a position he held until 1959. While at LSC, he spent summers doing research on optics, light, and lasers at the Naval Ordinance Test Center at China Lake. He worked with some of the most famous physicists of that time, including J. Rud Nielsen and Arthur Compton, a Nobel laureate. Thompson became a full-time researcher at China Lake in 1959 and worked there for fifteen years, retiring at age 73.

He and his wife retired to Lancaster, California, where he was living at the time of his death at 100.

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