[1] The current club was renamed in 2005, when it was promoted to the Vyscha Liha for the first time.

Originally the club entered the Ukrainian Professional League in the Druha Liha Group C in the 1999–2000 season as FC Arsenal Kharkiv.

After a 2nd-place finish in the 2004–05 Persha Liha, Arsenal Kharkiv was promoted to the Vyshcha Liha for the first time and prior to the season the club was bought by new management and they renamed the team to FC Kharkiv.

The newly established club presented three teams in the Ukrainian competitions, the senior squad competed in the Top League, the second team (FC Kharkiv-2) competed in the Second League, while another reserve squad (FC Kharkiv-d) competed in the special Reserve competitions.

The club struggled in the Premier League that season and eventually relegated to the Persha Liha.