The club was formed in 1893, by Lorraine 'Pa' Wilson. In 1907 they joined both the Isthmian League and the Spartan League, leaving the latter at the end of the 1907–08 season. In 1919–20 the club won its first Isthmian League title, winning the league on goal average against Nunhead. They also won the FA Amateur Cup, beating Tufnell Park 1–0 in the final at the Den.
The club won the league again in 1925–26, and the FA Amateur Cup for a second time in 1931–32 win a 7–1 win against Marine in the final. The following season the club won their third league title. In 1933–34 they reached the Amateur Cup final again, but lost 2–1 to Leyton. The two clubs met in the final again in 1936–37, with Dulwich winning 2–0.
In 1948–49 the club won the Isthmian League for a fourth time. A fifth Isthmian League title – in the restructured First Division – was won in 1977–78, but after several years of gradual decline, the club finished bottom of the Premier Division in 1989–90, and were relegated to Division One. They were promoted back to the Premier Division at the end of the 1991–92 season after finishing third in Division One. In 1998–99 the club reached the first round of the FA Cup for the first time since 1948, losing 1–0 to Southport.
After finishing bottom of the Premier Division in 2000–01, the club were relegated back to Division One. After finishing seventh in 2003–04, the club played off against Wealdstone for a place in the Premier Division after league re-organisation, but lost 5–4 on penalties after a 2–2 draw. In 2010–11 Dulwich finished fifth and entered the promotion play-offs, beating Bognor Regis Town 3–1 in the semi-finals before losing 4–3 to Leatherhead in the final. The following season the club finished third, again qualifying for the promotion play-offs. After beating Folkestone Invicta 2–1 in the semi-finals, they lost the final 1–0 to Bognor Regis. They returned to the Premier Division after winning the Division One South title on the last day of the 2012–13 season with a 1–1 draw against Burgess Hill Town.
After a 2-1 win to Workington on the last day of the 2013-14 season, they secured a play-off place, where they went onto win 4-1 on aggregate to Bognor Regis and they secured themselves a place in the Vanarama South after winning 2-1 in the play-off final to Kingstonian.