The Atoms were founded by Philadelphia construction mogul Thomas McCloskey in 1973 at the urging of Kansas City Chiefs and Dallas Tornado owner Lamar Hunt.

Playing a largely American line-up, they won the NASL title in their first year of existence by defeating Hunt’s Dallas club 2–0.

After this championship match, Philadelphia goalkeeper and Ridley Park, Pennsylvania native Bob Rigby became the first soccer player to be featured on the cover of Sports Illustrated.

Fielding a primarily Mexican side (almost 30 years before Chivas USA would try a similar approach in Major League Soccer), attendance continued to wane and the club folded after the 1976 season.

Although Clive Toye reports in his recent book that the franchise was sold to an ownership group from Montreal, he apparently confuses the fate of the next Philadelphia NASL team for that of the Atoms; the Atoms were, in fact, going to be relocated to San Antonio by their Mexican owners, who planned to replace the San Antonio Thunder franchise (which itself had just relocated to Honolulu to play as Team Hawaii).