| Station | Subway Transfers |
| Queens |
| Astoria-Ditmars Boulevard Subway Station | |
| Astoria Boulevard Subway Station | |
| 30th Avenue Subway Station | |
| Broadway Subway Station | |
| 36th Avenue Subway Station | |
| 36th Avenue Subway Station | |
| Queensboro Plaza Subway Station | |
| Manhattan |
| Lexington Avenue/59th Street Subway Station | |
| Fifth Avenue/59th Street Subway Station | |
| 57th Street-Seventh Avenue Subway Station | |
| 49th Street Subway Station | |
| Times Square-42nd Street Subway Station | |
| 34th Street-Herald Square Subway Station | |
| 28th Street Subway Station | |
| 23rd Street Subway Station | |
| 14th Street-Union Square Subway Station | |
| Eighth Street-New York University Subway Station | |
| Prince Street Subway Station | |
| from here on two types of services: via Montague Street tunnels for the night service and via Manhattan Bridge for other times. |
| The Night Service (via Montague Street Tunnels) |
| Canal Street Subway Station | |
| City Hall Subway Station | |
| Cortlandt Street Subway Station | |
| Rector Street Street Subway Station | |
| Whitehall Street-South Ferry Subway Station | |
| Brooklyn |
| Court Street Subway Station | |
| Jay Street-MetroTech Subway Station | |
| DeKalb Avenue Street Subway Station | |
| The Regular Service (via Manhattan Bridge Tunnels) |
| Canal Street Subway Station | |
| The Night Service via Montague Street Tunnels enter here |
| Atlantic Avenue-Pacific Street Subway Station | |
| Union Street Subway Station | |
| Ninth Street Subway Station | |
| Prospect Avenue Subway Station | |
| 25th Street Subway Station | |
| 36th Street Subway Station | |
| 45th Street Subway Station | |
| 53rd Street Subway Station | |
| 59th Street Subway Station | |
| Eighth Avenue Subway Station | |
| Fort Hamilton Parkway Subway Station | |
| New Utrecht Avenue Subway Station | |
| 18th Avenue Subway Station | |
| 20th Avenue Subway Station | |
| Bay Parkway Subway Station | |
| Kings Highway Subway Station | |
| Avenue U Subway Station | |
| 86th Street Subway Station | |
| Coney Island-Stillwell Avenue Subway Station | |