DH Cebu FC

The club is owned by Dynamic Herb Sports Incorporated, under the management of Ugur Tasci, a Turkish businessman who first arrived in the Philippines in 1994, together with his brother, Cem Tasci who developed Leylam Football Club that brought honors to Cebu in football tournaments, locally and abroad. Following the success of Leylam, Tasci formed a new club that would join the Philippines Football League. Leylam is considered as the predecessor of Cebu F.C.

Philippines Football League

In 2021, it was reported that the club would changed it name to Dynamic Herb Cebu and was applying for a license to be able to join the Philippines Football League as early as that season. On 31 July 2021, Dynamic Herb Cebu was granted a provisional license pending full compliance of requirements that would allow it to participate in the 2021 Philippines Football League season.

2021 season

Dynamic Herb Cebu's initial roster composed mostly of homegrown players from Leylam reinforced by players from other PFL clubs and collegiate teams. The club's provisional license was affirmed on 24 August 2021. The club was scheduled to debut in the 2021 PFL season, but the competition was cancelled due to the COVID-19 pandemic. The club played its first competitive match on November 11, 2021, a 1–0 loss to Stallion Laguna at the 2021 Copa Paulino Alcantara. Cebu qualified in the 2021 Copa Paulino Alcantara semi-finals as group runners-up. They lost to eventual champions Kaya-Iloilo 1–0 in the semifinals. Cebu finished their 2021 season as fourth placers in the Copa Paulino Alcantara after losing to Stallion Laguna via penalty shootout.

2022 season

After securing a partnership with Turkish Süper Lig club Hatayspor, Cebu signed Mehmet Kakil as the club's new head coach with Levent Öztürk as his assistant. They also signed former Hatayspor youth players Mert Altinöz and Arda Çinkir while Nazim Özcan was signed on loan.

Cebu started their 2022 season by defeating Stallion Laguna 2–0 in the 2022 Copa Paulino Alcantara, recording their first ever victory since the club's foundation. Cebu finished second in the table and captured a semi-finals berth for the second straight season. They lost to eventual champions United City 1–0 in the semifinals. Cebu once again finished as fourth placers in the Copa Paulino Alcantara after losing to Stallion Laguna 2–1.

Cebu made their Philippines Football League debut in a 3–0 defeat against Kaya-Iloilo.

AFC Cup debut

Cebu finished 2022–23 Philippines Football League season as runners-up thus seeing them qualified for their very first 2023–24 AFC Cup group stage competition. Cebu was than drawn in Group F alongside Australian club, Macarthur, Cambodian league champions, Phnom Penh Crown and Myanmar league champions, Shan United. On 26 October 2023, Cebu recorded their first ever continental win against Shan United in a 1–0 win with Ken Murayama scoring the only goal to give the club their first ever points in the AFC Cup.