Makhaya Ntini was born in Mdingi, a small village in Cape Province which is near King William's Town (currently in Eastern Cape province). He was discovered by a Border Cricket Board development officer who was setting up a mini-cricket programme. Although Ntini was both too old and too big to participate in the programme, the officer, Raymond Booi noticed the bared-footed cowherd's enthusiasm and talent for bowling. He lent the 15-year-old Ntini a pair of plimsolls and arranged for him to participate in a net session in King William's Town. Ntini impressed Booi, who contacted the head of the development programme, Greg Hayes, and the pair placed Ntini in a junior cricket festival in Queenstown. For the festival, Hayes purchased Ntini his first pair of boots – but later had to give the young bowler instructions not to wear them indoors, or when herding cattle.

Two years later, he was selected to tour England with the South Africa Under-19 squad, and played all five of the youth internationals. England dominated both One Day Internationals (ODIs) during the tour, with the South Africans only managing to take one wicket across the two matches, which fell to Pierre Joubert. In the Test series, which England won 2–0, Ntini claimed nine wickets, the second-most by a South African bowler. His bowling was expensive, coming at a rate of 4.53 runs per over: more than any other South African with the exception of Mark Boucher, who is best known as a wicket-keeper. After two matches for Border against the touring Kenyans,

Ntini made his first-class debut in November 1995, facing an England XI. He claimed two wickets in England's only innings as Border were beaten comprehensively.

In his debut season, Ntini claimed 17 wickets at an average of 37.05 in first-class competitions.