John McCandless Thompson (January 4, 1829 – September 3, 1903) was a Republican member of the U.S. House of Representatives from Pennsylvania.

He was a member of the Pennsylvania State House of Representatives in 1859 and 1860, and served one year as speaker.

He entered the Union Army during the American Civil War and served as major and subsequently as lieutenant colonel of the One Hundred and Thirty-fourth Regiment, Pennsylvania Volunteer Infantry.

Thompson was elected as a Republican to the Forty-third Congress to fill the vacancy caused by the resignation of Ebenezer McJunkin.

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