Flinders was born on 16 March 1774, the oldest of seven children, in the market town of Donington, Lincolnshire, England, the son of Matthew Flinders, a surgeon - apothecary, and his wife Susannah, (née Ward). His home, pictured, is no longer there although a similar building has been built on the site, bearing a plaque to commemorate his birth place.

 He was educated at Donington Free School, founded by Thomas Cowley in 1718 for preparatory education and at aged 12 moved as a boarder to Horbling Grammar School under the direction of Rev. John Shinglar. There he was introduced to the Classics and Mathematics, the grounding for navigation, which he acknowledged later in life.  His father expected his son to follow the family tradition of becoming a doctor, however from an early age, Flinders had been enthralled with Daniel Defoe's  tale of Robinson Crusoe and dreamed of distant lands waiting to be discovered. He  later wrote:
“I burned to have adventures of my own. I felt as I read that there was born within my heart the ambition to distinguish myself by some important discovery.”

He was largely self-taught, having studied Greek classics, navigation techniques, and Captain Cook's voyages of discovery. 

A cousin, who was the governess for the family of Captain Thomas Pasley (1734-1808), a highly regarded British Royal Navy officer, had mentioned Matthew's ambition to go to sea. On meeting Flinders, Pasley was highly impressed by the young man's wealth of knowledge.  

Once Flinders had enlisted in the Royal Navy, Pasley secured him a place aboard the HMS Alert - this would be the start of an illustrious naval career.