Plenty of local trains are available on the Central Railway line for Karjat from Mumbai, and from where starts your actual journey into this nature's paradise.
If coming from Pune, catch any Mumbai bound train and get off at Karjat (Around 95 kms from Pune).Then catch a CST bound local train from Karjat and get down at Neral (21 kms, would take around 15 min).
From Neral Station , there is a toy train which runs to Matheran about 4 times in a day. This toy train is not operational when railway route is under maintenance or when there is a perceived hazard e.g. the monsoons. Unfortunately, the only way to find this out is at the Neral Station.
Neral to Matheran tickets as of Novermber 2009 costs are 1st Class 210Rs, 2nd Class Reserved 35Rs, 2nd class unreserved 20Rs. Tickets can be booked from 3 to 1 day in advance, and then on the day of travel from 45 minutes before the train.
The train is often full, so turn up in good time to ensure you get a ticket. You can also book the ticket online through IRCTC. If there's a queue of unmoving people at the ticket window with a salesman who's reading the paper, then all the 2nd class tickets are sold out. Jump the queue to the window and ask for 1st class as the're usually available.