An attacking player of wide range, he operated in various positions on the right side of the pitch (right-back, midfielder or forward), and was best known for his Barcelona spell, during the club's Dream Team years.

[7][8] In 1990–91, Goikoetxea arrived at Camp Nou, joining several other Basque players including Begiristain, Andoni Zubizarreta, Julio Salinas and Bakero; these would help form the backbone of the legendary Dream Team, winning four league titles in a row and adding the club's first European Cup (where he appeared in the second half of the 1–0 win over UC Sampdoria).

[9] He also scored the winning goal in the subsequent edition of the UEFA Super Cup, won at the expense of SV Werder Bremen.

[14][15] Six years later he started his coaching career, always under his former Osasuna and Athletic teammate José Ángel Ziganda; the pair worked at newly promoted Xerez CD during the 2009–10 campaign, leaving in early 2010 due to poor results.

[18] During the 1994 competition in the United States, Goikoetxea appeared in all the matches, scoring twice in two draws against South Korea (2–2) and Germany (1–1), his misplaced crossing attempt catching goalkeeper Bodo Illgner off-guard in the latter game.