Southern Airways Express serves the following destinations:
| City | Airport | IATA Code | Destinations | Notes | 
|---|---|---|---|---|
|  Arizona | ||||
| Phoenix | Phoenix Sky Harbor International Airport | PHX | Imperial | |
|  Arkansas | ||||
| El Dorado | South Arkansas Regional Airport at Goodwin Field | ELD | Dallas/Fort Worth Memphis | EAS Community | 
| Harrison (AR) | Boone County Airport (Arkansas) | HRO | Dallas/Fort Worth Memphis | EAS Community | 
| Hot Springs | Memorial Field Airport | HOT | Dallas/Fort Worth Memphis | EAS Community | 
| Jonesboro | Jonesboro Municipal Airport | JBR | St. Louis Nashville | EAS Community | 
|  California | ||||
| Imperial | Imperial County Airport | IPL | Los Angeles Phoenix | EAS Community | 
| Los Angeles | Los Angeles International Airport | LAX | Imperial | Hub | 
| San Carlos | San Carlos Airport (California) | SQL | Santa Barbara Truckee | Branded as Surf Air | 
| Truckee | Truckee Tahoe Airport | TKF | San Carlos | Branded as Surf Air | 
|  Colorado | ||||
| Denver | Denver International Airport | DEN | Chadron | |
|  Illinois | ||||
| Chicago | O'Hare International Airport | ORD | Burlington (ended June 30, 2025) West Lafayette (ended August 4, 2025) Quincy | |
|  Iowa | ||||
| Burlington | Southeast Iowa Regional Airport | BRL | Chicago (ended June 30, 2025) St. Louis (ended June 30, 2025) | EAS Community | 
|  Indiana | ||||
| West Lafayette | Purdue University Airport | LAF | Chicago [1] (ended August 4, 2025) | Subsidized by Purdue University | 
|  Missouri | ||||
| St. Louis | St. Louis-Lambert International Airport | STL | Burlington (ended June 30, 2025) Jonesboro Quincy | |
|  Nebraska | ||||
| Chadron | Chadron Municipal Airport | CDR | Denver | EAS Community | 
|  Pennsylvania | ||||
| Bradford | Bradford Regional Airport | BFD | Pittsburgh Washington-Dulles | EAS Community | 
| DuBois | DuBois Regional Airport | DUJ | Pittsburgh Washington-Dulles | EAS Community | 
| Lancaster | Lancaster Airport (Pennsylvania) | LNS | Pittsburgh Washington-Dulles | EAS Community | 
| Pittsburgh | Pittsburgh International Airport | PIT | Bradford DuBois Lancaster | Hub | 
| Williamsport | Williamsport Regional Airport | IPT | Washington-Dulles [2] | |
|  Tennessee | ||||
| Memphis | Memphis International Airport | MEM | El Dorado Harrison (AR) Hot Springs | Hub | 
| Nashville | Nashville International Airport | BNA | Jonesboro | |
|  Texas | ||||
| Dallas/Ft. Worth | Dallas/Fort Worth International Airport | DFW | El Dorado Harrison (AR) Hot Springs | Hub | 
|  Virginia | ||||
| Washington, DC | Washington Dulles International Airport | IAD | Bradford DuBois Lancaster Williamsport | Hub | 
| City | Airport | IATA Code | Destinations | Notes | 
|---|---|---|---|---|
|  Alabama | ||||
| Birmingham | Birmingham–Shuttlesworth International Airport | BHM | Atlanta-Peachtree Destin Gulf Shores Panama City (FL) | |
| Gulf Shores | Jack Edwards Airport | GUF | Birmingham Memphis New Orleans-Lakefront | |
|  Arizona | ||||
| Show Low | Show Low Regional Airport | SOW | Phoenix [3] | EAS Community | Contract awarded to Contour Airlines due to poor reliability and service [4] | 
|  California | ||||
| Hawthorne (CA) | Hawthorne Municipal Airport (California) | HHR | San Carlos | Branded as Surf Air | 
| Santa Barbara | Santa Barbara Municipal Airport | SBA | San Carlos | Branded as Surf Air | 
|  Colorado | ||||
| Pueblo | Pueblo Memorial Airport | PUB | Denver | |
|  Florida | ||||
| Destin | Destin Executive Airport | DSI | Atlanta-Peachtree Birmingham Jackson (MS) Madison Memphis New Orleans-Lakefront Olive Branch (MS) Tampa | |
| Key West | Key West International Airport | EYW | West Palm Beach (temporarily suspended) | Weekend Service Only | 
| Panama City | Northwest Florida Beaches International Airport | ECP | Atlanta-Peachtree Birmingham Memphis-DeWitt Spain Memphis-Olive Branch New Orleans-Lakefront Oxford (MS) | |
| Tampa | Tampa International Airport | TPA | Destin West Palm Beach | Weekend Service Only For Destin | 
| West Palm Beach | Palm Beach International Airport | PBI | Key West Tampa | |
|  Georgia | ||||
| Atlanta | Hartsfield-Jackson Atlanta International Airport | ATL | Jackson (TN) | Hub | 
| Atlanta-Peachtree | DeKalb-Peachtree Airport | PDK | Destin Memphis | |
|  Louisiana | ||||
| New Orleans | Lakefront Airport | NEW | Destin Gulf Shore Memphis Oxford (MS) Panama City (FL) | |
|  Maryland | ||||
| Baltimore | Baltimore/Washington International Airport | BWI | Altoona DuBois Hagerstown Johnstown Lancaster Morgantown | Former Hub | 
| Hagerstown | Hagerstown Regional Airport | HGR | Baltimore Pittsburgh | Former EAS Community | Ended due to falling short of 10 passenger enplanement requirement and exceeding $200 subsidy cap. | 
|  Massachusetts | ||||
| Boston/Norwood | Norwood Memorial Airport | OWD | Nantucket | Ended due to lack of aircraft needed in other regions [5] | 
| Hyannis | Cape Cod Gateway Airport | HYA | Nantucket | Ended due to lack of aircraft needed in other regions [5] | 
| Nantucket | Nantucket Memorial Airport | ACK | Boston/Norwood Hyannis Lancaster New Bedford Providence | Hub | Ended due to lack of aircraft needed in other regions [5] | 
| New Bedford | New Bedford Regional Airport | EWB | Nantucket | Ended due to lack of aircraft needed in other regions [5] | 
|  Michigan | ||||
| Muskegon | Muskegon County Airport | MKG | Chicago | EAS Community | Community requested to terminate contract due to cancellation concerns, contract awarded to Denver Air Connection [6] | 
|  Mississippi | ||||
| Gulfport | Gulfport–Biloxi International Airport | GPT | Oxford | |
| Madison | Bruce Campbell Field | DXE | Destin Memphis | Service switched to Jackson International Airport | 
| Olive Branch | Olive Branch Airport | OLV | Atlanta-Peachtree Chattanooga Destin Gulf Shores Knoxville Panama City | Switched to Memphis International Airport | 
| Oxford | University-Oxford Airport | UOX | Destin Panama City Jackson Gulfport | |
| Jackson (MS) | Jackson-Evers International Airport | JAN | Destin Memphis | |
|  Nevada | ||||
| Las Vegas | Harry Reid International Airport | LAS | Imperial | |
|  New York | ||||
| Jamestown | Chautauqua County-Jamestown Airport | JHW | Pittsburgh | Former EAS Community | Below 10 passenger enplanement requirement and exceeded $200 subsidy cap. Attempting to reestablish EAS service with Boutique Air. [7] | 
|  Pennsylvania | ||||
| Altoona | Altoona–Blair County Airport | AOO | Baltimore Pittsburgh | EAS Community | Boutique Air awarded contract | 
| Franklin | Venango Regional Airport | FKL | Pittsburgh | Former EAS Community | Below 10 passenger enplanement requirement and exceeded $200 subsidy cap. | 
| Harrisburg | Harrisburg International Airport | MDT | Pittsburgh | |
| Johnstown | Johnstown-Cambria County Airport | JST | Baltimore Pittsburgh | EAS Community | Boutique Air awarded contract | 
| Wilkes-Barre | Wilkes-Barre/Scranton International Airport | AVP | Pittsburgh | |
|  Rhode Island | ||||
| Providence | T.F. Green Airport | PVD | Nantucket | |
|  Tennessee | ||||
| Chattanooga | Chattanooga Metropolitan Airport | CHA | Knoxville Memphis | |
| Jackson | McKellar-Sipes Regional Airport | MKL | Atlanta St. Louis | [8] | 
| Knoxville | McGhee Tyson Airport | TYS | Chattanooga Memphis | |
| Memphis | General DeWitt Spain Airport | - | Atlanta-Peachtree Destin Gulf Shores New Orleans Panama City | |
| Nashville | Nashville International Airport | BNA | Memphis | Ended due to low demand | 
|  West Virginia | ||||
| Morgantown (WV) | Morgantown Municipal Airport | MGW | Pittsburgh Washington-Dulles | EAS Community | Committee recommended SkyWest Airlines for new contract [9] | 
|  Guam | ||||
| Guam | Antonio B. Won Pat International Airport | GUM | Saipan | Branded as Marianas Southern Airways | 
|  Northern Mariana Islands | ||||
| Rota | Rota International Airport | ROP | Saipan | Branded as Marianas Southern Airways | 
| Saipan | Saipan International Airport | SPN | Guam Rota Tinian | Branded as Marianas Southern Airways | 
| Tinian | Tinian International Airport | TIQ | Saipan | Branded as Marianas Southern Airways |