He served in the American forces during Revolutionary War and later moved to Kentucky.

He commanded troops who on 1810 September 23 captured the Spanish fort in at Baton Rouge, commencing the West Florida Rebellion of 1810.

A few days later the West Florida Assembly, meeting at Saint Francisville, commissioned General Philemon Thomas to march the West Florida Army across the newly proclaimed Republic.

According to Southeastern Louisiana University history professor Sam Hyde, Philemon Thomas served in the War of 1812 and later served two terms in Congress.

In 1820, he was a member of the Electoral College, voting for James Monroe.