Born in Málaga, Andalusia, Castillejo graduated from Málaga CF’s youth system. He made his senior debut with the reserves in 2011, aged only 16, and went on to play three full seasons in Tercera División. He was given the nickname El Fideo (“the noodle” in Spanish), due to his “wiry frame and ability to squirm away in tight spaces”.
In June 2014, Castillejo was called up by first-team manager Javi Gracia for the pre-season. He was named man of the match in a 3–1 friendly win against Newcastle United where he scored twice. He was promoted to the main squad the following month.
On 29 August 2014, Castillejo made his debut with the first team, coming on as a substitute for fellow youth graduate Juanmi in the 57th minute of a 0–3 La Liga away loss against Valencia CF. He scored his first professional goal on 2 February, the winner in a home win over Valencia.
Samu Castillejo played total 39 matches for Malaga. On these matches Samu managed to score 1 goal and assist additional 5.
Castillejo joined Villarreal CF on 18 June 2015, signing a five-year deal, with his Málaga teammate Samu García. He scored six times in his third season, helping Villareal qualify for the UEFA Europa League after a fifth-place finish.
Castillejo played 127 matches for Villareal. On these matches he managed to score 11 goals and assist additional 15.