They won the championship of this league for five successive years in the early 1920s, after which they joined the Brighton & Hove District League in 1926. Just one year later, however, they joined the Sussex County League where they were to remain until 1972. The club became Bognor Regis F.C. in 1929 after King George V added the suffix ‘Regis’ to the seaside resort.

The club won the Sussex County Division One championship in the 1948–49 season. At the end of that season, they added “Town” to their name so as not to be confused with the local rugby club.

At the end of the 1969–70 season they were relegated, but won Division Two at the first attempt. The club won the Division One championship title the following season and were promoted to Division One South of the Southern League. In 1972–73 they reached the first round of the FA Cup for the first time, losing 6–0 at Colchester United. In 1976 Jack Pearce became manager at the age of just 26, and went on to hold the position until 2007.

In 1981 the club were transferred to Division One of the Isthmian League, and were promoted at the end of the 1981–82 season after finishing second. In 1984–85 they reached the first round of the FA Cup again, beating Swansea City 3–1 in a replay after a 1–1 draw at the Vetch Field. In the second round they lost 6–2 at Reading. They reached the second round again the following season, beating Enfield in the first round, before losing 6–1 at Gillingham. They went on to reach the first round again in 1986–87 (losing 1–0 in a replay to Slough Town) and 1987–88 (losing 3–0 at home to Torquay United). In 1988–89 they beat Football League opposition again, defeating Exeter City 2–1, before losing to Cambridge United.

In 1991–92 Bognor finished in the relegation zone, but were reprieved after Dagenham and Redbridge Forest merged. However, the following season they finished bottom of the Premier Division, and were relegated to Division One. In 1995–96 they reached the second round of the FA Cup for a fourth time, before losing 4–0 at Peterborough United.

In 2002–03 they finished second in Division One South, and were promoted back to the Premier Division. After finishing tenth the following year, the club were placed in the newly established Conference South. They were relegated back to the Isthmian League Premier Division at the end of the 2008–09 season, and were relegated again the following season.

Season 2010–11 saw the club compete in the Isthmian League Division One South and they missed out on promotion back to the Premier Division by the tightest of margins. Having finished with a club record total of 96 points, they lost out in the title race to Metropolitan Police on goal difference by just one goal, having led the table by two points, going in to the last fixture. As a result, they found themselves having to participate in the end-of-season play-offs, where they lost at home to Dulwich Hamlet who had finished 31 points behind. Revenge was sweet, however in the 2011–12 they again finished second in Division One South. They won the end-of-season play-offs, defeating Godalming Town in a thrilling semi-final, before beating Dulwich Hamlet 1–0 in the final, and thus gaining promotion to the Premier Division.