Changes from 2008
New franchises
- Twelve franchises joined the league this year, all expansion franchises:
| Team Name | Metro Area | Location | Previous Affiliation |
|---|---|---|---|
 Bay Area Ambassadors | San Francisco Bay area | Hayward, CA | expansion |
 Buffalo City | Buffalo area | Buffalo, NY | expansion |
 Chattanooga FC | Chattanooga area | Chattanooga, TN | expansion |
 Eau Claire Aris | Eau Claire area | Eau Claire, WI | expansion |
 Erie Admirals | Erie area | Erie, PA | expansion |
 FC Indiana | Indianapolis area | Muncie, IN | return from hiatus |
| NorCal Lamorinda United | Lamorinda area | Orinda, CA | expansion |
| Pocono Snow | Pocono Mountains area | East Stroudsburg, PA | expansion |
 Pumas FC | Greater Birmingham area | Birmingham, AL | expansion |
| Reading Revolution | Reading area | Reading, PA | expansion |
 Saturn FC | Marietta area | East Point, GA | expansion |
 Southern Oregon Fuego | Southern Oregon area | Medford, OR | expansion |
Name changes
- Princeton 56ers changed its name to Madison 56ers
Folding
- Seven teams left the league prior to the beginning of the season:
- Alabama Spirit - Birmingham, Alabama (never actually played an official NPSL game)
- Atlantic City Diablos - Atlantic City, New Jersey
- Lancaster Inferno - Salunga-Landisville, Pennsylvania
- Milwaukee Bavarians - Milwaukee, Wisconsin
- Performance FC Phoenix - Greenville, South Carolina
- Queen City FC - Buffalo, New York
- Santa Cruz County Breakers - Aptos, California [2]
- In addition, three 2008 teams either chose or were forced to spend the 2009 season on hiatus, with plans to return in 2010:
- Also, two teams which spent the 2008 season on hiatus did not return, and left the league permanently:
