They won the league at the first attempt to earn promotion to the Premier Division, also reaching the first round of the FA Cup, losing 1–0 at Wrexham.

In their first season in the Premier Division they finished fourth and reached the play-off final, where they lost 4–3 at Tonbridge Angels.

In 2012–13 Lowestoft reached the play-off final for the third consecutive season after finishing as runners-up, this time losing 2–1 at home to Concord Rangers.

After finishing mid-table in their first season and winning the Suffolk Premier Cup, beating Whitton United 2–1 after extra time, they were relegated from the renamed National League North at the end of the 2015–16 season, although they retained the Premier Cup with a 3–1 win over Leiston.

The club were transferred to the Premier Central division of the Southern League at the end of the 2017–18 season as part of the restructuring of the non-League pyramid.

In 1988, the 1885 pavilion was demolished and part of the site was sold to a developer, with the proceeds funding the building of a new changing room and hospitality block.

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.