In 1992–93, by now playing at the new Central Park ground, they won promotion to the Southern League Premier Division, however a financial crisis led to relegation two years later.

Although the team bounced back, winning the Southern Division title at the first attempt, they were relegated again in 1998 as the club hovered on the brink of being wound up completely.

A move out of Central Park and a drastic reduction in the playing budget saw the Brickies through their troubles, but they flirted with relegation back to the Kent League for a number of years, only finishing in the top half of the table on one occasion in the next eight seasons.

Joe Dowley resigned as manager after the last game of the 2011–12 season stating that he wished to return to his playing career.

A new squad was recruited and the season started on a positive note and at one point saw them reach the top of the table.

In January 2018 Nick Davis resigned and was replaced by one of the coaches, Aslan Ödev, as an interim manager for the rest of the season.

In January 2019 Aslan Odev left his position and was replaced by Chris Lynch the Dover Athletic head of youth development.

In January 2023, Ryan Maxwell was appointed manager of Sittingbourne, as well as the club's director of football.

Since 2018, Sittingbourne have enjoyed a mutual friendship with Danish 2nd Division club Fremad Amager, with the aim of establishing a strong and long-lasting “football friendship” and promoting unity and goodwill between the two sets of fans through a number of joint initiatives.

The club found it hard to guarantee the availability of the stadium due to the racing, however, and agreed to start playing their games on part of the complex where they used to train.

In March 2013 it was announced that they would leave Bourne Park at the end of the season for financial reasons and move to the Woodstock Park complex to share with Southern Counties East League side Woodstock Sports who themselves are now defunct.