Accounts differ, but Burke enlisted with 15th Regiment of the New York State Volunteers (N.Y.S.V.) on the 17 June 1861, and is in the roster titled 'Fifteenth engineers' among those published in 1893 and 1905. The 15th N.Y.S.V. received instruction in army engineering (they were known as "sappers") at Alexandria, Virginia and were associated with works like trenches, barriers, bridges etc. around various engagements including Yorktown, Gettysburg and Petersburg. He was never hurt: only 5 of the regiment died in action; 124 perished from disease etc. Devoy reported that he was demustered in Virginia on 13 June 1865, having been granted the rank of brevet colonel. John Joseph Corydon, a witness for the prosecution in his trial in London in 1868, said he knew Burke as a sergeant in the Federal army in 1862 and that Burke became a lieutenant, then a captain. This is confirmed in army records: one document held in public records in Chicago records him as a 2nd lieutenant (also held there is his citizenship document, dated 1865); the New York State Military Museum record indicates his sequence of ranks in different companies until - on 13 June - mustering out as captain at Fort Berry, Virginia.