Born in the Basque Country and raised in Valencia, Gaizka started his career at CD Tonin and later moved to CD Castellon. He played 17 games with the "Castelloneses" where he caught the eye of Valencia CF, who quickly moved to sign him as one of their own.
During his time at Valencia, Mendieta won the Copa Del Rey and the Supercopa de España. In 2001, he was signed by SS Lazio and later returned to LaLiga on loan to shine with FC Barcelona. After a year at the Camp Nou, he finished playing in the English Premier League and hung up his boots for good in 2008.