An enthusiast in several sports from a young age, Lizarazu began his professional career with Girondins de Bordeaux, joining the club's youth setup as a 15-year-old in 1984 and initially playing as a winger. After being told he would not make a career from football due to his frail physicality as a teenager, he impressed the staff with his determination and became a member of the senior squad in 1988 alongside forward Christophe Dugarry. He was retrained to play as a counter-attacking left back at the suggestion of coach Didier Couécou and soon replaced the veteran Gernot Rohr in the position. In 1990 Bordeaux finished runners-up in the French championship, but the following year they were administratively relegated amid financial problems. Lizarazu remained with the club and helped them immediately regain their top tier status in 1992. The club also signed Zinedine Zidane, who became another important element of the team, which went on to achieve two 4th- and a 7th-place finish over the next three seasons, Lizarazu contributing 101 appearances and 15 goals. In summer 1995, Bordeaux won the Intertoto Cup to qualify for the 1995–96 UEFA Cup. They would go all the way to the final under coach Rohr, beating Real Betis, A.C. Milan and Slavia Prague before losing to Bayern Munich 5–1 on aggregate. However their league form suffered, dropping to 16th. Following UEFA Euro 1996, in which Dugarry, Zidane and Lizarazu were part of the French squad which reached the semi-finals, the three moved abroad seeking a new challenge: Zidane joining Juventus, Dugarry going to Milan and Lizarazu staying local but changing nations by moving to Athletic Bilbao, based the same distance from his home in the French Basque Country as Bordeaux. He appeared 299 times for his formative club, scoring 28 goals.
Athletic Bilbao
Lizarazu spent just one season with the La Liga club after becoming the first Frenchman to play for Athletic, which has a policy of selecting only players of Basque birth or heritage. Suffering from a persistent groin injury, he was unable to displace the experienced Aitor Larrazábal at left back, received two red cards among the 16 league appearances he did make, and had disagreements with the head coach, compatriot Luis Fernández. In the 1997 close season, he transferred to Bayern Munich.
Bayern Munich
Before even playing a Bundesliga match, Lizarazu lifted a trophy with his new club, winning the inaugural edition of the preseason DFL-Ligapokal. It was the start of a highly successful spell in Bavaria, despite the interruption of some serious injuries, as he went on to win six Bundesliga championships, as well as five DFB-Pokals, the Champions League in 2001, and the Intercontinental Cup. On winning the Intercontinental Cup in 2001, he became the first player to be a current European and World champion in both club and international football. Lizarazu said that he would leave Bayern in the summer of 2004 and eventually signed with Olympique Marseille. However, after only six months back in France, he returned to Bayern Munich in January 2005. During his second spell with Bayern, ending in 2006 when he gave way to the emerging Phillipp Lahm, Lizarazu wore the shirt number 69; clarifying that it was not a lewd gesture, he said this was because he was born in 1969, his height is 1.69 m and he weighed 69 kg. He made 268 appearances in all competitions for Bayern between 1997 and 2006, scoring eight goals. 183 of these games were in the German top-flight.
International career
Lizarazu was capped 97 times for France, scoring two goals, and helped them win the 1998 FIFA World Cup and Euro 2000, starting in the final of both tournaments. He retired from international football after France were surprisingly eliminated by eventual winners Greece at Euro 2004.