Filipov started his career in Spartak Varna's youth and made his debut for the club's first team at the age of 19 on 14 February 2004 in a 3–0 defeat to Belasitsa Petrich.
In June 2010, Filipov signed a two-year contract with newly promoted A PFG side Kaliakra Kavarna.
On 31 July he scored Kaliakra's first ever A PFG goal, in the 1–0 win over Slavia Sofia on the opening day of the 2010–11 season at the Ovcha Kupel Stadium.
One month later Filipov scored his third goal for Kaliakra in the third round of the 2010–11 Bulgarian Cup, a 3–1 defeat to Pirin Blagoevgrad at Hristo Botev Stadium.
Manager Radostin Trifonov later said he expected Filipov to be absent for a minimum of six months.