Stephen Gilbert was born on 13 May 1878 at Burpham, Sussex, the middle of five children of John Gilbert, a groom, and his wife Harriett.

He joined the Royal Navy training ship HMS NORTHAMPTON on 28 January 1895, giving his previous occupation as gardener. After various training and harbour service drafts, he joined the pre-dreadnought battleship HMS RESOLUTION in September 1896 and remained there until the start of 1899, being rated Able Seaman in September 1898. After drafts to EXCELLENT and VERNON, he joined the monitor HMS MAGDALA in January 1900, which served as a floating defensive battery for Bombay harbour. On return to Britain a year later he rejoined HMS RESOLUTION until she paid off in October 1901 when the crew transferred to the new battleship HMS FORMIDABLE then proceeding to the Mediterranean. He was promoted to Leading Seaman in November 1904 and was employed as a Leading Torpedoman.

In July 1905 he joined the submarine depot ship HMS THAMES, and alternated between her and the depot ship HMS MERCURY for the next five years.  It is not known which submarines he served in. In 1908 he re-engaged to complete 22 years service and in the autumn of 1910 he was drafted to HMS BALMORAL CASTLE which served as a temporary Royal Yacht, carrying the Duke and Duchess of Connaught for the inauguration of the Union of South Africa. After short periods in VERNON and EXCELLENT, he joined the cruiser HMS VENUS.  In November 1912 he returned to HMS DOLPHIN where he remained until leaving the Royal Navy on a free discharge on 12  April 1913.

He joined the Royal Australian Navy (on the books of the London depot) on 15 April 1913 and was promoted to Petty Officer (Leading Torpedoman) on 1 June. The following year he was among the crew that took HMAS AE2 (in company with AE1) from Portsmouth to Australia, at the time the longest ever voyage undertaken by submarines. His RAN record notes that in September 1914 he took part in operations in German New Guinea, where AE1 was lost. At the end of 1914, AE2 was sent to the Mediterranean and, on 25 April 1915, was the first submarine to penetrate the Dardanelles. After five days however, AE2 was attacked by Turkish forces and forced to surface. The submarine was abandoned and scuttled and the crew were taken prisoner. Petty Officer Gilbert was one of four members of the crew who subsequently died in captivity.  His official date of death is 9 October 1916; however, one report from a fellow prisoner indicates that he may have died earlier on 26 September.

He left a widow, Beatrice Alice (née Hatcher) whom he had married in 1905, and a daughter, Florence, born in 1907. They had moved to Croydon, a suburb of Sydney, New South Wales.

Stephen Gilbert was originally buried at Belemedik, Pozanti, Turkey and a photograph exists of his original grave surrounded by a wooden fence, taken as part of a 1919 Australian Red Cross investigation. However he was re-interred and is commemorated at Baghdad (North Gate) War Cemetery.