| Thomas M. Wagner | |
| Birth Date: | ca. 1824 |
| Birth Place: | Charleston, South Carolina, US |
| Death Place: | Fort Moultrie, Sullivan's Island, South Carolina, US |
| Placeofburial: | St. Michael's Churchyard in Charleston, South Carolina |
| Allegiance: | Confederate States of America |
| Serviceyears: | 1861 - 1862 |
| Rank: | Lieutenant Colonel |
| Commands: | 1st South Carolina Artillery |
Thomas M. Wagner (c. 1824 – July 17, 1862) was an American military officer, who held the rank of lieutenant colonel in the Confederate Army during the American Civil War. He was killed when a cannon exploded during an inspection at Fort Moultrie. The main fortification on Morris Island was subsequently named for him and was the site of the First and Second Battle of Fort Wagner.
Before the war, he was a South Carolina state senator and an executive of the Charleston and Savannah Railroad.