Getting to Uppsala couldn't be easier, with regular trains from Stockholm throughout the day in 40 minutes. This means that trains from the north of Sweden towards Stockholm also all stop here so it is equally easy to get here from for instance Gävle. Many trains also stop at Stockholm Arlanda airport on the way to and from Stockholm as the airport is as close to Uppsala as it is to Stockholm.
The SJ train Stockholm-Uppsala is the best and most reliable way to go to this lovely city. They have 2 departures every hour most of the day.
Besides this way, you can also take the Upptåget train. This one you take in Upplands Väsby and will make a quick stop at Arlanda. Convenient for you who are staying in Väsby or close to it. And last but not least, there's always a bus from Swebus, but I haven't taken it so I can't comment.
There are a lot of trains going everyday from Stockholm to Uppsala. There are X2000 high speed trains, but less expensive 'normal trains are also very fast and efficient. If you want to see a time table just visit the website of SJ. On the pic you can see my friend Marie eating a DAIM icecream in the train on the way back from Uppsala. She won't be too happy seeing this pic here I guess...haha
I came to Uppsala by train from Stockholm and left the town 4 days later on the same route. During the day the two cities are connected by at least one train per hour; at peak times even more.
The trip takes 38 minutes and in October 2013 a single ticket cost 108 SEK at the train station (SJ counter) or 84 SEK if bought online.
I also used the train from Uppsala to Knivsta, where I had to catch a bus to Sigtuna for a plesant side trip. Please read more about this in my "Off the beaten path" tips.
Uppsala's modern train station (Central station) is located right in the city centre, so that most sights and accommodation can easily be reached on foot.
By the way, the trains are not as accurate and punctual as they are in Switzerland because i arrived few minutes late on Stockholm Station becuase of traffic but i luckily found the train which was late. but i recommend you to avoid any such adventure :-)
Trains leave from / to Stockholm pretty often & a one-way ticket costs around 70 SEK. Note that the price may vary if you buy the ticket in Uppsala or in Stockholm. And be sure to use you ISIC or any student card! The schedules change around mid August & beginning of January every year!
Getting to Uppsala from Stockholm Railway station is an easy task since traffic is regular. Don't forget to bring Id/passport before buying a ticket. You need to show ID with ticket at the train.
There is very good express train connection between Uppsala & Stockholm. I paid a student fare of 120 Swedish Kronor (return). The trains run after every 20 mins between these countries till late at night.
From Arlanda Airport there are busses as well as trains every half an hour. Very handy and good priced. Takes you to Uppsala in 20 mins.
Bus or bike is the best way to get around in Uppsala and surrounding.
If you arrive in Sweden by plane, you will probably land at Arlanda Airport. From here you can either go directly to Uppsala by train or by bus. Or you can start in Stockholm and take the train to Uppsala from there, for the day or a few days. The trainride from Arlanda is about 20 minutes, and from Stockholm it's about 40 minutes. Cost: Around 7,5 US$
When in Uppsala, you can actually walk most places, the town center is not very big. For sightseeing outside the immediate center, the town buses are the best means of transportation. They are green(see pic), and run everywhere in town, and on and around the central square 'Stora Torget' (litt. the Big Square) is where all the lines meet.