Born in Madrid, Juanfran joined local Getafe CF's youth ranks aged 17, making his senior debut in 2007 with the reserves in the Tercera División.

[4] After one year with Villarreal CF's reserves in the Segunda División B, which ended in promotion, a first-ever for the team, Juanfran returned to his hometown and signed with Real Madrid.

Juanfran made his debut with the first team on 2 May 2010, replacing Fernando Gago in a home league fixture against CA Osasuna, with five minutes to go: the score was then at 2–2, but the Merengues eventually won 3–2 thanks to a Cristiano Ronaldo goal.

[11] The following summer, even though newspaper La Voz de Galicia initially reported an agreement had been reached to a permanent four-year deal after the English club received a compensation,[12] he was again loaned to the Spaniards who now had a buying option.

[15] On 29 July 2019, Juanfran rescinded his Deportivo contract with a year remaining by mutual consent to join Alanyaspor of Turkey's Super Lig,[16] signing a two-year deal with the option of a third the same day.