John Pipon was the youngest son of Col James Kennard Pipon, Seigneur of Noirmont, and Elizabeth Collier, daughter of John Collier MP. He was born in Malta and educated at Wellington College. He joined the Navy at the age of 13 and was commissioned as sub-lieutenant six years later and promoted Lieutenant in 1872.
He was Lieutenant on the Royal Yacht Victoria and Albert and promoted commander in 1880.
He was married on 28 December 1882 at St Mary's, Stone, near Dartford, Kent, by the Rev J. C. C. Pipon, his brother, to Alice Elizabeth Johnson, eldest daughter of Murray M. Johnson, of Stone Castle, near Dartford. THey had two sons, James and Henry, who both joined the Navy.
At the time he was commander of HMS Penelope, which had been involved in the bombardment of Alexandria earlier in the year.
While the off-shore squadron was engaging the forts at long-range, HMS Monarch, HMS Penelope and HMS Condor were ordered into close engagements with the forts at Maza-el-Kanat and Fort Marabout.
His next command was HMS Ranger, which involved him in the defence of Sudan's Red Sea port Suakin in 1885 and then took him to the Burmese War.
He was promoted Captain on 1 January 1887 and three years later took command of HMS Magicienne.
In 1891 he was appointed British Consul at the Portuguese port of Beira in East Africa and was rewarded for his work there with a CMG. Three years later he commanded HMS Sirius, in which he was senior British officer on the South American Atlantic coast when revolution in Rio de Janeiro put British lives and property at risk.
He was made Companion of the Bath at Queen's Victoria's Diamond Jubilee and was appointed her ADC in 1899, also taking up the command of HMS Caesar in the Mediterranean shortly before his death on 6 May that year.