After a brief passage at Real Madrid's academy he made his senior debut with neighbours CD Leganés, scoring five goals in 37 games in an eventual 2004 relegation from the Segunda División.

Borja moved to Real Valladolid in summer 2005, but could only appear for its reserves during his spell, being loaned to Alicante CF in his second year after which he was released.

[2] On 27 October, he scored twice against Real Madrid in the Copa del Rey in a final 4–0 home rout, taking his tally against this club to six (he had netted already four times in different editions of the tournament); Alcorcón won 4–1 on aggregate.

[3][4] On 16 August 2012, it was announced that Borja had signed for Scottish Premier League side Kilmarnock on a one-year deal, after spending some weeks on trial.

[9] Having gone scoreless in his season in the Canary Islands, Borja played out the last two years of his career with smaller teams in his native region, CF Fuenlabrada (third tier) and UD San Sebastián de los Reyes (Tercera División).