He was a Captain of Foot in the Low Countries 1585-1589 as part of the English Army allied with the Dutch against the Spanish. John Scott was knighted in 1588 in the Low Countries by Lord Willoughby.
He married firstly Elizabeth Stafford, widow of Drury, and secondly Katherine (Smythe) Hayward, daughter of Thomas (Customer) Smythe. There is no known issue from either marriage.
There appears to have been a close relationship between John Scott and the brothers of his second wife, Katherine Smythe. Sir John Scott was appointed a co-executor of the will of his brother in law, Roberte Smithe, gentleman of London, the will made on 01 Dec 1600 and proved on 28 Jan 1600/1601. Robert referred to him as his wellbeloved brother in law and bequeathed to him his Italian and French books.
In Feb 1601, Sir John Scott along with his brother in law, Sir Thomas Smythe, became caught up in the Rebellion against aging Queen Elizabeth I led by Robert Devereux, Earl of Essex. However, both men managed to clear themselves of direct involvement.
Scott was a member of the Board of the the Virginia Company in 1607, the Company headed by Sir Thomas Smythe. Scott was a co-executor of the will of his brother-in-law, Sir John Smythe, and in the will of Sir Richard Smythe made 11 years after the death of Sir John Scott, Sir Richard bequeathed to his son two velvet footcloths, “whereof one was given unto me by Sir John Scott knight deceased". In his own will, Sir John Scott noted his ‘ancient, approved and most faithful friend’ Sir Thomas Smythe.
Sir John Scott was the junior MP for Kent, 1604-1611 and for Maidstone, 1614-1616.
Sir John Scott died childless at his Kent estate in Nettlestead after a short illness in September 1616. His heir was Elizabeth Scott, the 12-year old daughter of his deceased younger brother Richard Scott. She married Thomas Dereham, Baronet, on Jan. 1, 1602 in London.. Scot's Hall went to his younger brother Sir Edward Scott.
A portrait of Sir John Scott from 1603 is held at the North Carolina Museum of Art. 
In the Scott Chapel at Brabourne Church, Kent, is a tablet as follows “Here liest the body of Sir John Scott, son of Sir Thomas Scott, Justice of the Peace, and Captain of a Company …. Troop of Lancers. AD 24 Sep 1616. This monument was placed here by appointment of his brother, Sir Ed. Scott, Knight of the Order of the Bath”.
A memorial service to celebrate the lives of Sir John Scott and Lady Katherine (Smythe) Scott (on the 400th anniversary of their deaths) was held at St Mary's the Virgin church, Nettlestead, Kent, England, UK, on 25 Sep 2016, with the Rt Revd James Langstaff, Lord Bishop of Rochester.
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