Surabaya - Jakarta

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There are 2 stations in Surabaya.
Surabaya Pasarturi trains head West, it only serves a few trains to Jakarta.
Surabaya Gubeng trains go South, this is the main station.

You can get through Surabaya and go straight into Jakarta on the overnight train.

There are no sleepers on Indonesian trains but they are air conditioned.

You do have a few options for getting to Jakarta, at the upper end of comfort is the KA1/KA3 train, know as the "Argo Anggrek"

KA3 Surabaya 2200 | Jakarta 0600
KA1 Surabaya 0800 | Jakarta 1800

There are a total of 3 night trains plying the way along this route.

KA 35 1920 | 0600 (KA SEMBRANI)
KA 73 1745 | 0515 (KA GUMARANG)

There is some wonderful scenery along the way, alot of it is on the southern side of Java. To see it you need to take the more leisurely trip via Bandung.

KA5A Surabaya Gubeng 0720 | Bandung 1940 (KA ARGO WILIS)
Overnight in Bandung
KA21 1430 | Gambir 1713 (KA ARGO LAWU)

Bandung is a university town and uses a system of minibuses called angkot

One of the good things is that the Indonesian network is predominantly passenger trains, due to the limitations of the rail infrastructure and relative short distances between major centers.