The station is owned and operated by PT Kereta Api Indonesia.

Sembrani has all executive (first class) train set and provides the fastest traveling time to Jakarta and Surabaya.

The only intercity train that does not stop at Bojonegoro station is Argo Bromo Anggrek.

Bojonegoro railway station is also served with some regional rail services that operate between small towns and cities with more stops over shorter distances than intercity rail services.

[9][10] Since 9 August 2016, all passengers must check themselves in and print boarding passes at self-service check-in machines (Indonesian: mesin check-in mandiri) before boarding in addition to showing tickets and valid identifications (e.g. Kartu Tanda Penduduk/KTP, Surat Izin Mengemudi/SIM or passport).