Panayotov began his career at Levski Sofia, but he never made a first team appearance. However, he played regularly for the club with the under-19s. Panayotov went on loan to B PFG side Volov Shumen at the start of the 2009–10 season.
In June 2010, he moved to Pirin Gotse Delchev. He scored once in 16 appearances, before moving to Bansko in January 2011.
On 16 January 2017, Panayotov signed with Stal Mielec.[3]
On 19 June 2017, Panayotov moved to Levski Sofia.[4] He left the club at the end of the 2017–18 season when his contract expired.[5]
On 7 August 2018, Panayotov signed with Cherno More for two years.[6] On 17 August, he made his official debut in a 0–0 home draw against Beroe Stara Zagora.[7]