In 1983 Grays transferred to Division Two of the Isthmian League. League reorganisation saw them placed in Division Two South in 1984 and they went on to win the division at the first attempt, earning promotion to Division One. In 1987–88 they were Division One runners-up, resulting in promotion to the Premier Division. In 1988–89 the club reached the first round of the FA Cup for a second time, losing 2–0 at Bath City. They remained in the Premier Division until being relegated back to Division One at the end of the 1996–97 season. In 1999–2000 the club were Division One runners-up, earning promotion back to the Premier Division. In 2000–01 another appearance in the FA Cup first round saw them play Football League opposition for the first time, losing 4–0 at Reading.