In his country, he played professionally for Málaga B, Málaga, Gimnàstic and Racing de Santander, amassing La Liga totals of 106 games and six goals over the course of five seasons. In 2009 he signed for Rubin Kazan, remaining in the Russian Premier League until his retirement.
Born in Móstoles, Community of Madrid, Navas was brought through the ranks of hometown's Real Madrid, but only played with its B-team. He made his La Liga debuts in the 2004–05 season, going on to spend two years in the competition with Málaga CF: his first match was on 12 December 2004, as he featured the full 90 minutes in a 1–0 home win against Levante UD.
In January 2007, Navas left Málaga and the second division and played for six months on loan with top flight strugglers (eventually relegated) Gimnàstic de Tarragona. After his return to Andalusia he had a trial with English club Ipswich Town, but an eventual deal fell through due to a metatarsal injury; he subsequently joined Racing de Santander also in the top level, signing for two years.
A habitual starter throughout the first half of the 2008–09 campaign, Navas was sold in late February 2009 to Russia's FC Rubin Kazan, on a three-year deal worth €2 million. He appeared in 28 games in his first year, as the team renewed their Russian Premier League supremacy.
On 12 July 2015, 35-year-old Navas signed a one-year contract with FC Rostov, agreeing to an extension one year later.