Johnston resigned from the Army in March 1837 and studied civil engineering. During the Second Seminole War, he was a civilian topographic engineer aboard a ship led by William Pope McArthur. On January 12, 1838, at Jupiter, Florida, the sailors who had gone ashore were attacked. Johnston said there were "no less than 30 bullet holes" in his clothing and one bullet creased his scalp, leaving a scar he had for the rest of his life. Having encountered more combat activities in Florida as a civilian than he had previously as an artillery officer, Johnston decided to rejoin the Army. He departed for Washington, D.C., in April 1838 and was appointed a first lieutenant of topographic engineers on July 7; on that same day, he received a brevet promotion to captain for the actions at Jupiter Inlet and his explorations of the Florida Everglades.