In these last two seasons at the top level, notable players included midfielder Miguel Ángel Portugal and defender Antonio García Navajas, both of whom later signed with Real Madrid.

After a doubtful first year, where the club avoided relegation in the last weeks of the competition, Burgos CF started to qualify to the promotion play-offs to Segunda División.

In the 2001–02 season, with Enrique Martín as head coach, Burgos would finish 16th but they would be relegated to Segunda División B due to the non-conversion of the club into a Sociedad Anónima Deportiva.

[2] After this administrative relegation, Burgos would continue playing in Segunda División B, being very close to promotion in the 2007 play-offs, where they were beaten by Sevilla Atlético in extra time of the last round.

[3] Burgos would spend three seasons in Tercera División after its promotion in the 2011 play-offs, where they beat UD Lanzarote by 4–0 in the second leg played at El Plantío.

[4] On 19 June 2017, one month after avoiding the relegation to Tercera División by winning Linares Deportivo in the play-offs, the assembly of Burgos CF approved the conversion of the club into Sociedad Anónima Deportiva, 16 years later after the first frustrated attempt.

[6] On 4 June 2019, Burgos CF signed an affiliation agreement with CD Nuestra Señora de Belén, for acting as its women's football section.