Under coach Choo Seng Quee, the club won the inaugural President's Cup in 1968, then reached and lost the next two finals.

[3] The club was officially renamed as Lion City Sailors and its signature red colour was replaced with white and blue.

The Sailors' main aim following its rebranding was to boost professionalism in Singaporean football, with becoming a Southeast Asian super club its long-term goal.

As it sets its sight on success in 2020, Lion City Sailors will be led by Australian head coach, Aurelio Vidmar, the former Socceroos captain.

He joins after a hugely successful stint in Australia where he led Adelaide United to the 2008 AFC Champions League final, becoming the first Australian team to earn this distinction.

Vidmar make a couple of stud signings including Singaporean stars, Hassan Sunny, Gabriel Quak and Shahdan Sulaiman, Japanese defender Kaishu Yamazaki, as well a prolific Australian striker, Andy Pengelly.

With the motivation to rejuvenate the glory days of the past into the future, On 18 May 2021, Kim Do-hoon, who led Korea Republic's Ulsan Hyundai to victory in 2020 AFC Champions League, joined the Sailors on a two-and-a-half-year deal.

Sailors maiden AFC Champions League campaign ended with narrow 2–1 to Daegu in the final group stage fixture.

The Football Association of Singapore (FAS) handed a three-match ban with immediate effect, with Kim being fined $2,000 and Fahrudin $3,000, for their violent conduct.

Less than 24 hours after Kim was handed a three-match suspension and fine for violent conduct, Lion City Sailors made the shock announcement that they have reached a "mutual agreement" to part ways with the Korean coach.

The Sailors embarked on their second consecutive AFC Champions League appearances ahead of their 2023–24 campaign together with Jeonbuk Hyundai Motors, Bangkok United and Kitchee which will see a return of home and away fixtures.

The club hosted most of the AFC Champions League group stage games at the Jalan Besar Stadium as its match the requirements standard of the tournament and also being rated as a FIFA 2 Star Recommended Turf.

On 8 November 2023, the Sailors defeated two-time AFC Champions League winners Jeonbuk Hyundai Motors 2–0, with Živković scoring both goals.

On 4 May 2024, they won their third Singapore Community Shield after beating Albirex Niigata (S) 2–0, with Shawal Anuar and Maxime Lestienne scoring to secure the win.

The Sailors will also compete in both the inaugural 2024–25 AFC Champions League Two and the recently revived 2024–25 ASEAN Club Championship tournament.

At a home game against Thai side Port on 5 December 2024, Song Ui-young scored a hat-trick which secured a 5–2 win seeing Lion City Sailors qualifying to the round of 16 as group leaders making them the first ever Singaporean Club to do so.

[8][9] In June 2020, the launch of the new Lion City Sailors Football Academy was announced, along with further plans on youth development and its investments.

[12] On 29 July 2022, Lion City Sailors officially opened its new S$10 million training centre boasting the finest facilities in the football ecosystem in Singapore.

[16] The commitment saw a series of youth development programmes, coaching, educational and professional exchanges as well as football training camps in Germany.

[17] In 2022, Lion City Sailors and 16-time Eredivisie champions, Feyenoord Rotterdam forged a 3-year partnership focused on youth development and education.

[18] The commitment will see a series of youth development programmes, coaching, educational and professional exchanges as well as football training camps in the Netherlands, with Sailors supporting Feyenoord's brand exposure in Singapore.