Born in Bera, Navarre, Fagoaga joined SD Eibar in 1999, after spending four seasons at Antiguoko; he was initially assigned to the reserves in Tercera División.
[2][3] After becoming a permanent first team member ahead of the 2002–03 season, Fagoaga scored his first professional goal on 21 December 2004, netting the opener in a 2–1 home loss also against Recre.
[10] On 21 September 2014, he took over the Juvenil squad,[11] before being named at the helm of the farm team CD Vitoria on 9 January 2019, replacing sacked Igor Gordobil.
[15] He left the club by mutual consent the following 27 April, after a run of four defeats in the last five league games of the campaign, which saw the side miss out on the play-offs by six points.
[17] On 1 December 2023, however, he left the club to join Beñat San José's staff as an assistant manager at Liga MX Atlas FC.