Scruton was born in Buslingthorpe, Lincolnshire, to John "Jack" Scruton, a teacher from Manchester, and his wife, Beryl Claris Scruton (née Haynes), and was raised with his two sisters in High Wycombe and Marlow. The Scruton surname had been acquired relatively recently. Jack's father's birth certificate showed him as Matthew Lowe, after Matthew's mother, Margaret Lowe (Scruton's great grandmother); the document made no mention of a father. However, Margaret Lowe had decided, for reasons unknown, to raise her son as Matthew Scruton instead. Scruton wondered whether she had been employed at the former Scruton Hall in Scruton, Yorkshire, and whether that was where her child had been conceived.
Jack was raised in a back-to-back on Upper Cyrus Street, Ancoats, an inner-city area of Manchester, and won a scholarship to Manchester High School, a grammar school. Scruton told The Guardian that Jack hated the upper classes and loved the countryside, while Beryl entertained "blue-rinsed friends" and was fond of romantic fiction. He described his mother as "cherishing an ideal of gentlemanly conduct and social distinction that ... [his] father set out with considerable relish to destroy".
The Scrutons lived in a pebbledashed semi-detached house in Hammersley Lane, High Wycombe. Although his parents had been brought up as Christians, they regarded themselves as humanists, so home was a "religion-free zone". Scruton's, indeed the whole family's, relationship with his father was difficult. He wrote in Gentle Regrets (2005): "Friends come and go, hobbies and holidays dapple the soulscape like fleeting sunlight in a summer wind, and the hunger for affection is cut off at every point by the fear of judgement."
After passing his 11-plus, he attended the Royal Grammar School High Wycombe from 1954 to 1962, leaving with three A-levels, in pure and applied mathematics, physics, and chemistry, which he passed with distinction. The results won him an open scholarship in natural sciences to Jesus College, Cambridge, as well as a state scholarship. Scruton writes that he was expelled from the school shortly afterwards, when during one of Scruton's plays the headmaster found the school stage on fire and a half-naked girl putting out the flames. When he told his family he had won a place at Cambridge, his father stopped speaking to him.
Having intended to study natural sciences at Cambridge, where he felt "although socially estranged (like virtually every grammar-school boy), spiritually at home", Scruton switched on the first day to moral sciences (philosophy); his supervisor was A. C. Ewing. He graduated with a double first in 1965, then spent time overseas, some of it teaching at the University of Pau and Pays de l'Adour in Pau, France, where he met his first wife, Danielle Laffitte. He also lived in Rome. His mother died around this time; she had been diagnosed with breast cancer and had undergone a mastectomy just before he went to Cambridge.
In 1967 he began studying for his PhD at Jesus, then became a research fellow at Peterhouse, Cambridge (1969–1971), where he lived with Laffitte when she was not in France. It was while visiting her during the May 1968 student protests in France that Scruton first embraced conservatism. He was in the Latin Quarter in Paris, watching students overturn cars, smash windows and tear up cobblestones, and for the first time in his life "felt a surge of political anger":
I suddenly realised I was on the other side. What I saw was an unruly mob of self-indulgent middle-class hooligans. When I asked my friends what they wanted, what were they trying to achieve, all I got back was this ludicrous Marxist gobbledegook. I was disgusted by it, and thought there must be a way back to the defence of western civilization against these things. That's when I became a conservative. I knew I wanted to conserve things rather than pull them down.