At the age of 15, Estrada moved from his native Puerto Peñasco to Hermosillo to focus on his boxing career.

He defeated Manuel Almendariz by TKO for the WBC Mundo Hispano super flyweight belt.

Later that year, Estrada participated in the boxing reality show Campeón Azteca: Round 3 that took place between September and December 2011 in Tuxtla Gutiérrez.

Later on, with both fighters trading punches in the final round, Sánchez was rocked by a left hook from Estrada.

Sánchez attempted to get up but the referee waived the count, giving Estrada the win by TKO with 1:02 elapsed in the tenth and final round.

On November 17, 2012, Estrada moved down from his natural division to challenge WBA light flyweight champion Román González.

[9] In his first defense, he defeated number one ranked challenger and future champion Milan Melindo by unanimous decision (118-109, 118–109, 117–109).

[11] After spending a year away from the ring, Estrada came back against gatekeeper Raymond Tabugon in October 2016 in his native Puerto Peñasco.

[12] On fight night, Cuadras seemed to gain the upper hand in the early rounds, switch-hitting and throwing and landing more punches.

Nevertheless, Estrada was able to slowly impose his methodical style in the second half of the fight, even dropping Cuadras in round 11.

[17] On December 8, 2018, Estrada stepped in on short notice and fought Victor Mendez at super bantamweight.

[19] Gonzalez was expected to face Juan Francisco Estrada in a trilogy bout in the main event of a DAZN broadcast card on 5 March 2022, at Pechanga Arena in San Diego, California.

On 3 September 2022, it was announced that Gonzalez would face Juan Francisco Estrada for the third time in his professional career on 3 December.

The bout headlined a DAZN broadcast card, which took place at the Desert Diamond Arena in Glendale, Arizona.

[20] On June 29, 2024 in Phoenix, AZ, Estrada defended his WBC super flyweight title against Jesse Rodriguez.