||His first career was in the British Army. He trained at the Royal Military Academy, Sandhurst in 1979, and joined the Irish Guards. Lowther-Pinkerton served with the 1st Battalion Irish Guards, but was attached to the Special Air Service (SAS) throughout his 20-year army career, where he was described as an especially capable officer. He retired from the Army in 1998.
He served as Equerry to Queen Elizabeth The Queen Mother 1984-1986, and was promoted to Captain on 8 June 1986. He was a troop commander of the SAS as a Captain. He served in the first Gulf War in 1990-1991 as Special Forces Liaison Officer with United States forces., 
He was promoted to the rank of Major on 30 September 1992, and was in charge of two 20-man SAS counter-narcotics operations in Colombia for two years in the early 1990s. He attended the Staff College, Camberley, and qualified as a staff officer (psc). Lowther-Pinkerton was Commanding Officer of G Squadron SAS. In the mid-to-late 1990s he was in the Balkans for the strategic policy review by the Ministry of Defence; reportedly in 1994 as part of a four-man SAS "Joint Communication Organisation" in Bosnia., 
In 2001 he co-founded and has since been a director of Objective Travel Safety, which provides risk assessment training for young travellers and journalists. He trained Ewan McGregor and Charley Boorman for their Long Way Round and Long Way Down TV series. He is a part-time consultant to Kroll Risk Management, London., 
He was appointed Member of the Royal Victorian Order (MVO) for his service as Equerry to The Queen Mother in 1986, Member of the Order of the British Empire (MBE) in 1990 for service with the special forces in Colombia, and Lieutenant of the Royal Victorian Order (LVO) in the 2013 New Year Honours.
He is married to Susannah Lowther-Pinkerton (born Susannah Lucy Richards) with four children. The family lives in Suffolk. His ten-year-old son, William "Billy" Lowther-Pinkerton, was one of the pageboys at the wedding of Prince William and Catherine Middleton in April 2011.