In 1861, at the start of the Civil War, he was appointed by commander of New York National Guard, Brigadier General John F. Rathbone, to serve as chief medical officer at Albany depot. In June 1862, following Battle of Savage's Station, as Army of the Potomac, along with its physicians, retreated, Swinburne remained to care for the thousands of wounded prisoners, both Union and Confederate. Respecting his principled stand, Confederate commander Stonewall Jackson gave him a pass, with an accompanying personal note, permitting visits to Union prisoners. In 1864, Governor Horatio Seymour nominated him to the post of Health Officer of the Port of New York and, in 1867, he was renominated by Governor Reuben Fenton, serving a total of six years, until 1870. During his administration, despite the state legislature's reluctance to assign funding, he supervised the construction of then-state-of-the-art quarantine facilities on islands which were named Swinburne and Hoffman.