Swettenham joined the Straits Settlements civil service in January 1871. In 1872 he was posted to Penang and Province Wellesley to work in the land offices. In 1874 he assisted Governor Sir Andrew Clarke in resolving conflict among groups of Chinese tin-miners in Perak. At the same time, Clarke endorsed Raja Abdullah's claim to the title of sultan when he agreed to appoint a British resident, whose advice was to be accepted on all matters not involving Malay custom and religion. These terms formed the basis of the Pangkor engagement of January 1874, drafted in both Malay and English, with Swettenham's aid as an interpreter.

During 1875-86, Swettenham distinguished himself in the pacification of Perak following the murder of its first British resident. In March 1876 he was appointed assistant colonial secretary in Singapore. Swettenham next served as resident of Selangor and acting resident of Perak, before becoming resident in 1889. Following the federation of Malay states, Swettenham was made first resident-general in 1896. In 1901 he was appointed Governor of the Straits Settlements, and occupied the post until his retirement in 1904.