Panthrakikos Football Club was first established in 1963, as the result of a merger between Orpheas Komotini and Athlitiki Enosis Komotini. The team has risen to prominence in Greece in recent seasons, completing a dramatic climb through the divisions.
From their foundation year up until 1969, Panthrakikos competed regionally before entering the national league system. Over the course of the next few decades, the club bounced between the second and third tiers several times. During the 1980s, the team briefly fell as far as the fourth tier. In 1996, Panthrakikos merged with Orfeas Xylagani and competed under the name Panthrakikos Xylagani. The Xylagani section of the name was dropped in 1998. During the late 1990s and early 2000s, the club fell out of the professional league system, dropping to the amateur ranks.
The team's rise back through the divisions started with promotion to the fifth tier ahead of the 2002–03 season. In 2004, local entrepreneurs made a significant investment in the club and by 2006–07, Panthrakikos were competing in the Beta Ethniki, the second division. At the end of the 2011–12 season, the club were crowned champions of the division. In the process, they gained promotion to the top flight of Greek football for the first time in history. The 2012-13 season saw the team finish in 10th place, with the club retaining their top flight status.
Kostas Vasilakakis is one of the most notable players to have represented the club, while Nikos Soultanidis, Abdul Diallo and Bertrand Robert have been amongst the team's top goal scorers in recent seasons. Their current captain is Greek defender Achilleas Sarakatsanos.
The Municipal Athletic Centre of Komotini serves as Panthrakikos' home ground. The venue was built in 1922 has undergone renovations several times since. Until recently, it was able to hold just 3,000 supporters, but its capacity currently stands at 6,198.