The season began on May 2, 2009, and ended with the NPSL Championship Game in August 2009.
Sonoma County Sol finished the season as national champions, beating Erie Admirals 2-1 in the championship game on August 1, 2009.
[1] Purple indicates division title clinched Yellow indicates team received playoff spot Note: Charm City deducted nine points for failing to fulfil its last three fixtures.
Note: Boston deducted three points for failing to fulfil its last fixture.
Note: Indiana deducted six points for failing to fulfil its last two fixtures.