| Station | Subway Transfers |
| Queens |
| Forest Hills-71st Avenue Street Subway Station | |
| 67th Avenue Subway Station | |
| 63rd Drive-Rego Park Subway Station | |
| Woodhaven Boulevard Subway Station | |
| Grand Avenue-Newtown Subway Station | |
| Elmhurst Avenue Subway Station | |
| Jackson Heights-Roosevelt Avenue Subway Station | |
| 65th Street Subway Station | |
| Northern Boulevard Subway Station | |
| 46th Street Subway Station | |
| Steinway Street Subway Station | |
| 36th Street Subway Station | |
| Queens Plaza Subway Station | |
| 23rd Street-Aly Avenue Subway Station | |
| Subway Station | |
| Subway Station | |
| Manhattan |
| Lexington Avenue-53rd Street Subway Station | |
| Fifth Avenue/53rd Street Subway Station | |
| 47th-50th Streets-Rockefeller Center Subway Station | |
| 42nd Street-Bryant Park Subway Station | |
| 34th Street-Herald Square Subway Station | |
| 23rd Street Subway Station | |
| 14th Street Subway Station | |
| West Fourth Street-Washington Square Subway Station | |
| Broadway-Lafayette Street Subway Station | |
| Essex Street Subway Station | Between Broadway-Lafayette Subway Station and Essex Street Subway Station, the M Train changes railroad directions. The southbound service leaving Broadway-Lafayette Subway Station becomes northbound services entering Essex Street Subway Station, and vice versa. |
| Brooklyn |
| Macy Avenue Subway Station | |
| Hewes Street Subway Station | |
| Lorimer Street Subway Station | |
| Flushing Avenue Subway Station | |
| Myrtle Avenue Subway Station | |
| Central Avenue Subway Station | |
| Knickerbocker Avenue Subway Station | |
| Myrtle-Wyckoff Avenues Subway Station | |
| Queens |
| Seneca Avenue Subway Station | |
| Forest Avenue Subway Station | |
| Fresh Pond Road Subway Station | |
| Middle Village-Metropolitan Avenue Subway Station | |