Born in Villanueva de la Serena in the Province of Badajoz, Pajuelo was an academy player for hometown club CF Villanovense.[2] He made his debut aged 16 on 12 October 2003 as a last-minute substitute in a 3–0 home loss to Vecindario in the third-tier Segunda División B. He made two more appearances off the bench as the team were relegated to the Tercera División.[3] Pajuelo combined his football career with working as an insurance agent.[4]
In October 2015, before facing Barcelona in the last 32 of the Copa del Rey, Pajuelo told national newspaper El Mundo "I don't want to leave [Villanovense], it's a feeling. I feel comfortable, it's my town, I defend my team. Every footballer wants something more, but for me to leave Villanovense, it has to be to something bigger. But there's no place like home".[5] In the first leg on 28 October, he captained the club to a goalless draw against the La Liga opponents;[6] his team lost the second leg 6–1 at the Camp Nou.[4]
In 2016–17, Pajuelo played 33 games including the playoffs and scored once, as Villanovense made the semi-finals for promotion to the Segunda División.[7] Following the elimination by Racing de Santander, he extended his contract.[7]
Villanovense faced a top-flight opponent again in the last 32 of the Copa del Rey in 2018–19, namely Sevilla. Pajuelo's side taunted their visitors with a poster with the slogan "You have five [UEFA Europa League titles] but we have [Pajuelo wearing number] six".[8] In the first leg on 1 November, he missed an open goal with a header in a goalless draw;[9] Sevilla won the second leg at the Ramón Sánchez-Pizjuán Stadium with a goal by André Silva.[10]
Having not scored a goal in the third division since November 2018, 35-year-old Pajuelo netted in two consecutive games in January 2023, as his team won their first three games of the calendar year.[2] In June, approaching two decades since his debut, he extended his contract for another year.[11]
On 10 March 2024, Pajuelo played his 500th game for his club, a 1–0 home loss to fellow Extremadurans Navalcarnero.[12] He renewed his contract in June 2025, with the team having been relegated to the fifth-tier Tercera Federación after losing a playoff to Real Madrid C.[13] The city council in Villanueva de la Serena unanimously awarded Pajuelo its Sirena de Oro award on 30 January 2026, describing him as a "sign of sporting identity".[14]