Undrafted by any NHL team, in 2004, Penner signed with Anaheim after playing college hockey at the University of Maine in the National Collegiate Athletics Association (NCAA).

Growing up in Winkler, Manitoba, Penner played for his high school hockey team, the Garden Valley Collegiate Zodiacs, alongside future Washington Capitals teammate Eric Fehr.

He was scouted by Grant Standbrook, the assistant coach for the University of Maine's Black Bears ice hockey team,[4] and was offered a scholarship, which he accepted.

[2] Although he did not initially join the team, in the 2003–04 season, he helped lead the Black Bears and to the NCAA Championship game, scoring the game-winning goal in the semi-finals against Boston College.

[6] During the Mighty Ducks' 2006 Stanley Cup playoff run, Penner scored 9 points in 13 games until Anaheim was eliminated by the Edmonton Oilers in the Western Conference Finals.

Penner earned a full-time roster spot with the Ducks in 2006–07 and broke out with 29 goals and 45 points playing with Ryan Getzlaf and Corey Perry on a unit dubbed the "Kid Line".

He then began the 2008–09 season with a slow start and was publicly criticized by head coach Craig MacTavish for a lack of fitness and competitiveness after being made a healthy scratch for the second consecutive game.

[1] Penner was confirmed to be a part of a planned summertime 2009 blockbuster trade that would see Andrew Cogliano, Ladislav Šmíd and himself dealt to the Ottawa Senators in exchange for disgruntled All-Star forward Dany Heatley.

Penner is the 21st NHL player to play for both sides of the "Freeway Face-Off" between the Anaheim Ducks and the Los Angeles Kings, and the only one to win the Stanley Cup with both teams.