Born in Bergara, Gipuzkoa, Garitano was an Athletic Bilbao youth graduate. He made his senior debut with the reserves on 2 September 1989, starting and scoring the winner in a 2–1 away win against Racing de Santander for the Segunda División championship.
After four full seasons (one of them on loan at SD Eibar), Garitano left the Lions and signed for Cartagena FC in Segunda División B. In 1994, he moved to Cádiz CF also in the third level, and returned to Eibar in January 1996.
Garitano subsequently resumed his career in the third tier and Tercera División, representing CF Gavà, Racing de Ferrol, Burgos CF, Alicante CF and Benidorm CF. He retired in 2003 at the age of 33, mainly due to injuries.
Shortly after retiring, Garitano started working as an assistant manager at former club Alicante. In October 2008 he was named manager, replacing fired José Carlos Granero; however, after only three matches, he was replaced by Nino Lema and moved to the backroom staff.
On 6 April 2010, Garitano was appointed CD Castellón manager, after being previously working at the club as an assistant. He remained in charge until the end of the season, suffering relegation.
On 7 July 2011, Garitano signed with third division side Orihuela CF. The following campaign, also as manager, he worked with CD Alcoyano, eventually losing promotion with both teams in the play-offs.
On 28 June 2013, Garitano was named manager of CD Leganés still in the third tier. In his first season, he achieved promotion to the second level after defeating CE L'Hospitalet in the play-offs; another promotion followed in 2016, after finishing second in the regular season.As of 20 September 2017