[3] For the 2008–09 NBA season he joined several other fellow Spaniards in the league that included Pau and Marc Gasol, Jose Calderón, and Trail Blazers teammate Sergio Rodríguez.

[4][6] Fernández played in his first regular-season NBA game on 28 October 2008, coming off the bench to score 16 points in a 96–76 Portland loss to the Los Angeles Lakers.

[7] On 12 November 2008 Rudy scored 25 points in 29 minutes against the Miami Heat, including 8 of 8 from the free throw line adding to his already 92% FT shooting to set a new NBA career high.

[8] On 18 January 2009 it was announced that Fernández had won the fan voting and was picked the fourth dunker to go to the NBA Slam Dunk Contest as part of the 2009 All-Star Weekend.

[12][13] On 9 March 2009, against the Los Angeles Lakers, Fernández was taken off the court in a stretcher after Trevor Ariza hit him on the head on a fastbreak attempt.

Fernández was alert and conscious when leaving the court with full movement of his extremities, however, he was taken to the hospital due to chest pain.

[20] Fernandez along with teammate Patty Mills donated 50% of the proceeds from their jerseys sales, throughout the month of January, to help those affected by the floods in Australia.

Fernández struggled offensively for a good part of the year, but his improved play in other areas of the game has earned him praise from his peers.

Blazers head coach Nate McMillan, who isn't known to hand out compliments easily, singled out his defensive play in the second half of Game 4 against the Mavericks as the key to the 84–82 win.

[24] On 21 September 2011 Fernández signed a one-year contract with the Liga ACB team Real Madrid, valid only while a new NBA collective bargaining agreement remained under negotiation.

[25] Fernández signed for a reported salary of 2.7 million euros net income per season, the largest contract in Spanish league history, at that time.

[29] On 4 July 2012 Fernández returned to Real Madrid by signing a three-year deal[30] worth 9 million euros net income.

Fernández scored 22 points in 18 minutes of play, with 5 three-point goals, and completed a dunk over Dwight Howard[41] that ESPN sportswriter Bill Simmons described as "hellacious".

Spain won its inaugural gold medal in a European Championship, and Fernández averaged 13.2 points, 3.5 rebounds, 2.1 assists, and 2.1 steals per game, in 28.4 minutes, and was named to the All-Tournament Team.

In the 2010 FIBA World Championship, Fernández averaged 15.6 points, 6.0 rebounds, 1.7 assists, and 1.8 steals per game, but Spain only took sixth place in the tournament.