Travelling by train between the 2 largest cities in Lithuania is quite simple and straightforward.
You need to keep an eye on the timetables though but they seem to run to schedule pretty well.
There are two types of train. A fast one and a slow one and the times vary between just over an hour to 1hr 45m depending on which train you get. The faster train is slightly more expensive than the slower one.
I took both types of trains and they're both fine but the faster one makes more sense if you've got a limited amount of time - and is more comfortable.
My first experience with Lithuanian train was very positive. The ride was very smooth and comfortable. The scenery was nice. The restroom was clean. And best of all, the price of the ticket was very very affordable. That makes train travel in Lithuania a compelling choice. A friend of mine has recently traveled the similar trip and wrote a little blog about his travel here: http://europetrekking.wordpress.com. It covers his own experience with Lithuanian train of the same destination.
I took the train to & from Kaunas from Vilnius.
It was quick, comfortable and good value. The express services take 65 minutes - check in advance to avoid the slower services.
It was €6.37 each way. They don't seem to do return or discounted tickets (but you pay a bit extra if you buy your ticket on the train).
The station has been renovated and sparkles. You could eat your lunch off the floor.
Staff have been renovated too, and sparkle. Friendly, helpful and easy to deal with.
The downside is that the station is a good way out of the city centre. Plenty of city buses go past the stations towards the centre, of course.
I used the train to get from Kaunas to Vilnius. The journey was an 1h 25min pleasant ride and costed only 15 Ltl which is ~4 Euro.
I post the link to the railway company here.
Travelling by train is easy to and around Vilnius. As a student with an ISIC card you get 50% discount. But it is already cheap without discount. You can get from the airport to Vilnius, you have to buy a ticket in the train. If you did not buy a ticket at the station where it is possible you get a penalty of 5 Lt.
Although the Lithuanian railways are quite limited and some trains are a bit old, train is still the fastest means of transport to move throughout the country.
From Vilnius, you can take the express train to Klaipeda, calling at Siauliai and other minor towns, or one of the newer regional trains to Kaunas.
Vilniaus geležinkelio stotis, or Vilnius Train Station, is located at Geležinkelio gatvė 16, south of the city center. While buses are more popular and frequent to most destinations, trains are a viable option to get to some other parts of Lithuania, such as Trakai, Kaunas, and Klaipeda. There are daily connections to Moscow, St. Petersburg, Minsk, and Kaliningrad, but no direct connections to Warsaw or Riga as of 2012. (NOTE: there is an EU project underway to create a rail link from Tallinn to Warsaw through Riga and Kaunas, with a projected completion date of 2020) A daytime connection to Warsaw is possible with a change of trains in Sestokai and Kaunas, travel time approximately 9 hours. If you want to take the train to Riga, an overnight stay in Daugavpils, Latvia is required.
Inside the station, there are some services, to include ticket windows, a tourist office with extremely friendly but not terribly knowledgeable staff, and a grumpy "travel agent" whose sole purpose is to sell visas to those wishing to go to Russia and/or Belarus.
Ground transportation at the train station is plentiful. The plaza in front of the station entrance is served by Trolleybuses 1,2,5,7,16, and 20, as well as Buses 1, 1A, 3, 12, 13, 16, 19, 23, 26, 31, 34, 41, 42, 54, and 75. Fare starts at 2.2 Litas with a pre-paid travel card (These can be purchased many news stands and kiosks for 4 Litas). Alternatively, you can purchase a single-ride ticket from the driver for 2.5 Litas.
To get to Vilnius Airport (oro uostas), you have the choice of Bus 1 outside the station running roughly every 15 minutes, or an "Express train" running every 45-75 minutes to the airport. Fare for the train is 2.5 Litas.
We decided to return to the airport by train as it was quick, cheap and we wanted to travel on a train in Lithuania!
We understood that you could purchase tickets on board, but were directed to the ticket office by the woman at Tourist Information.
Luckily there wasn't a queue as our train departed in just over 5 minutes time. Our fare was 2.50Lt each for the 7 minute journey.
The information board was quite easy to read, but the ticket seller shouted 7 and raised 7 fingers to indicate the platform. Well we got there with a few minutes to spare and settled into our seats. The train was noticeably very clean.
Surprisingly this Lietuvos geležinkeliai service runs just once every hour, although we had allowed PLENTY of time to get to the airport - 4 hours as it turned out!
The train departed on time, and we were soon pulling into the airport station - Oro Uostas. It was a short walk from the station to the departures hall of the airport, on a canopied path
Like most of the Baltics, Lithuania doesn't have an extensive train network. Most of your journeys are best taken by bus. But the station is convenient for a couple of places: Daytripping to Trakai and the short trip on the new railway line to Kaunas. The train I took to Kaunas was brand new, clean, comfortable and on time.
A note for those with wheelchairs or prams: The station does have an elevator, but good luck getting access to it. We happened upon it by chance by asking at the information desk (to a woman who spoke only Russian). After shouting at me in Russian (I didn't understand) she begrudgingly sent for another woman who kindly showed us the lift. It was behind a locked door. After the locked door there was a sign, impossible to see from outside the locked door, written only in English and Russian (not Lithuanian), saying "ask at the information desk for access".
The station is a fair walk from the centre, about 10-15 minutes, but can be reached by pretty much all the buses that pass near the old town. Just look out for the Stotis stop.
On our first day in August 2006 we left Vilnius by regional train to Kaunas. This route is served more than 10 times per day. The trip took about 1,5 hours and cost 10,40 Litas (about 3,10 Euro; 2006).
Other domestic trains go to Klaipeda (7 h), Siauliai (4,5 h) and Trakai (40 mins). International services include Minsk (BY), Warsaw (PL), St. Petersburg and Moscow (RUS).
Vilnius' train station (Gelezinkelio Stotis) is located south of the Old Town, just next to the bus station.
Vilnius is the perfect hub to explore the rest of Lithuania, and the train is the best way to do so. Cheap by Canadian/American/Austrailian/British/Euro-using EU citizen expectations, and very comfortable. Has a very extensive inter-city network, and there are currency exchanges/ATMS nearby for various international currencies. I also used it to get to the airport, although I don't believe the train is as extensive as the bus/trolley network within Vilnius.
If you're headed to St Petersburg from Vilnius (or the other way around), be prepared. First, it's important to note that only one train leaves from Vilnius to St Petersburg daily. On even-numbered days, the route goes through Belarus, and you must have a Belarusian visa to take this train, even if you're just passing through on the way to St. Petersburg. A much better option is to leave on an odd-numbered day, when the route goes through Latvia instead, so no visa is required (except to enter Russia, of course). The train ride takes approximately 14 hours and goes over night. With all the border stops and passport/visa checks, don't expect to get a lot of sleep.
A warning: we had a very difficult time finding someone at the Vilnius train station who spoke English. Go in with some basic phrases ready and your information written down in Lithuanian, if possible (date traveling, destination, 1st vs. 2nd class wagon, etc).
My #1 recommendation: pay the extra money for a 1st class sleeper cabin. We went for 2nd class and couldn't ask what this would be like because train station employees spoke so little English. The 2nd class sleeper is nothing more than 40 or so bunk beds in an open wagon. There is absolutely no privacy, and we were nervous about sleeping with our belongings out in full view. This didn't end up being a problem, but I'd still highly recommend the upgrade. If you do end up in the 2nd class wagon, at least ask for a bottom bunk, which will make life easier.