After a playing career that ended at the age of 30 due to a knee injury, and with the biggest accomplishment being appearing for Rayo Vallecano in Segunda División, Chaparro began his senior coaching career with Extremadura CF also in that level. He subsequently moved to the lower leagues where he worked with Cádiz CF, Granada CF and Écija Balompié (where he would serve in several capacities and in different seasons) and Xerez CD back in division two, before arriving at Andalusia neighbours Real Betis' youth academy.
Subsequently, Chaparro worked as an assistant at the Verdiblancos. In the final day of the 2006–07 season he replaced sacked Luis Fernández at the helm of the first team, leading it to a 2–0 away win against Racing de Santander as the club narrowly avoided La Liga relegation. The reserves, which he also coached, would manage to promote to the third level.
Chaparro returned to the B's for the 2007–08 campaign, but was again called for main squad duties after Héctor Cúper only managed 11 points from 14 matches. His first game in charge was a 1–0 success at Villarreal CF, Betis retained their top flight status and he had his contract renewed for another year.
- Paco Chaparro: bético, entrenador y runner (Paco Chaparro: bético, manager and runner); Runner's World, 12 February 2008 (in Spanish)
- Racing Santander 0–2 Real Betis; ESPN Soccernet, 17 June 2007
- Paco Chaparro salva a Lopera (Paco Chaparro saves Lopera); 20 minutos, 18 June 2007 (in Spanish)
- Paco Chaparro toma hoy las riendas del equipo (Paco Chaparro takes reins of team today); Mundo Deportivo, 4 December 2007 (in Spanish)
- El Betis destituye a Paco Chaparro (Betis fire Paco Chaparro); Libertad Digital, 6 April 2009 (in Spanish)