Newton started his career at second-tier Charlton Athletic and worked his way up to the first team, making his debut as a 17-year-old on 14 August 1993 as a substitute in a 1–0 win over Birmingham City. He quickly became a first-team regular and was a virtual ever-present between 1995 and 1998. He was part of the team that reached the 1996 First Division play-offs, scoring inside the first minute of the first leg, which Crystal Palace won 3–1 on aggregate. This era also saw him recognised by his country as he won three England Under-21 caps during 1996. His debut came in a 2–0 win over Moldova U-21 on 31 August 1996.