The Timbers joined the PDL in 2009, and played their first ever game on May 9, 2009, against fellow expansion franchise Victoria Highlanders. The game finished 2-2, with the first goal in franchise history being scored by Jarad Van Schaik. The Timbers went on to enjoy a successful first season, eventually finishing second in the PDL Northwest division behind the Kitsap Pumas. The campaign was highlighted by several spectacular victories, including an 8-2 demolition of the Yakima Reds in late May in which seven different players got on the scoresheet, a 4-2 win over Cascade Surge which saw the Timbers score twice in the last six minutes to snatch the victory, and a high-scoring 4-3 win over Tacoma Tide which saw six goals in the first half. The Timbers lost the influential Warren Ukah to the pro-ranks half way through the season, but this did not stop the team enjoying a 5-game unbeaten run to finish the regular season which was capped off by a comprehensive 5-0 demolition of the Abbotsford Mariners on the last day of the season. Unfortunately for the Timbers they fell at the first hurdle in the playoffs, losing 3-2 to the Seattle Wolves after being 2-1 ahead with 9 minutes left, before allowing Seattle striker Alex Chursky to score twice in the dying moments, including an agonizing 90th minute winner. Ryan Youngblood was by far Portland's top marksman, finding the net 11 times, while Brent Richards contributed 4 assists.
The 2010 season saw the Timbers get off to a strong start, defeating the Washington Crossfire 3-1 in their opener on May 15. They continued their strong play, running off a string of six consecutive shutouts before finally allowing a goal in a 4-1 defeat of the Abbotsford Mariners on June 19. The Timbers continued their run, capping off a perfect regular season (16-0-0) with a 1-0 win at the Kitsap Pumas. Entering the playoffs as the #1 seed, the Timbers traveled to Bremerton, Washington for the Western Region finals. They advanced to the Championship round with 2-1 victories over the Hollywood United Hitmen and the host Pumas. The 2010 PDL Championship Series was held August 6–7 at PGE Park in Portland, Oregon. The participating teams were the Timbers as Western Champions, the Central Champions Thunder Bay (ON) Chill, the Baton Rouge (LA) Capitals as the Southern Champions and Reading United AC of Pennsylvania as the Eastern Champions. The opening round saw the Timbers defeat Reading and Thunder Bay win over Baton Rouge by identical 2-1 scores. On August 7, behind two goals from 2010 PDL Most Valuable Player Brent Richards, the Timbers defeated Thunder Bay 4-1 to become the first undefeated and untied champion in USL Professional Development League history
This list of notable former players comprises players who went on to play professional soccer after playing for the team in the Premier Development League, or those who previously played professionally before joining the team.