- Shushary customs station
- Southern customs station
- Vasileostrovsky customs station
- Petrodvortsovy customs station
- Northern customs station
- ‘Avtomobilny Zavod’ customs station
- Kolpino customs station
- Volkhov customs station
- Gatchina customs station
- St. Petersburg customs station (electronic declaration center)
- Pushkinsky customs station
- Pargolovsky customs station
- Yaninsky customs station
In 2013, due to the reorganization and liquidation of regional customs administrations, customhouses and customs stations, St. Petersburg Customhouse was joined by the customs stations located in:
- Novgorod Region: Novgorod, Novgorod (electronic declaration center), Chudovsky, and Borovichsky customs stations;
- Vologda Region: Vologda, Cherepovetsky, Cherepovetsky (electronic declaration center), and Vytegorsky customs stations;
- Komi Republic: Vorkuta, Zheshartsky, Syktykvkar, Usinsky, Ukhtinsky, and Ezhvinsky customs stations.