Although his age made him ineligible to enter the 2005 AFL Draft, Selwood's accomplishments during the year led to AFL Talent Manager Kevin Sheehan rating him "the best 17-year-old in Australia". Bendigo Pioneers regional manager Ray Byrne noted that "ability-wise, Joel was streets ahead of everyone. Even at an early age, he was a standout". Byrne praised Selwood's professionalism, writing that he had "never seen a kid prepare in the TAC Cup like Joel [Selwood]. He had a fantastic football brain, he could sort it out within 10 minutes of a game who should be where and (doing) what". Selwood received an array of accolades and honours as a bottom-aged player, winning mid-year State honours for Victoria Country in the AFL National Championships. His performances in the championships earned him end-of-year All-Australian honours and the Most Valuable Player award for Victoria Country. In addition, he was named in the TAC Cup Team of the Year, awarded a scholarship within the prestigious AIS-AFL Academy, and subsequently captained his older teammates in the annual under-18s International Rules Series in Ireland. His performances in Ireland earned him the Ron Barassi Medal, as the adjudicated Most Valuable Player of the tour. Selwood's achievements in local football were recognised when he was listed as a finalist in the 2006 Bendigo Sports Star of the Year Award.
Returning in 2006 with the Pioneers, Selwood entered his final year of junior football as one of the top rated prospects in his age group. His achievements at the junior level were recognised early by the AFL Players Association, when he was awarded the Mike Fitzpatrick Scholarship, and the AFL Life Members Education Fund Award. Rewarded with the captaincy of Bendigo for his final season, Selwood again won mid-year State honours for Victoria Country. However, a knee injury occurred only six rounds into the competition forcing him to undergo surgery—his fourth knee operation within two years—prematurely ending his season.
Selwood was drafted by the Geelong Football Club with their first selection, and was the seventh overall draft pick in the 2006 AFL Draft. Although many recruiting scouts viewed him as "the finest pure footballer in the draft", and a potential top pick, there was still concern surrounding the durability of his knee. Nonetheless, as the equal highest-ever draft pick for the Cats, Selwood made his debut in the opening round of the 2007 AFL Season and missed only four games during the regular season.