Balakov made 92 appearances for Bulgaria, between 1988 and 2003 (one of the best totals in national history) and scored 16 goals. He made his debut on 2 November 1988, in the 1–1 draw with Denmark in a qualifying match for the 1990 FIFA World Cup, coming on as a late second half substitute for Hristo Stoichkov. Other than the 1994 FIFA World Cup, he also played for his country at Euro 1996 and the 1998 FIFA World Cup. At age 37 he played in the qualifications for Euro 2004 to help his teammates qualify but retired from football before the final stage in Portugal.