Look at these sites to compare offers:
So maybe you should think about taking the train if you will not have to make any stops on your way. It is convenient and as fast as going by car. From Vienna Westbahnhof the subway U3 would take you into the historic city center in about 15 minutes.
The advice given to look to companies such as Gemut or Auto Europe for best prices is excelent . Most say they get best prices and little extras with these firms rather than booking direct with major firms.
many postings on Trip Advisor and other travel sites by happy renters with good experiences.
You still pick up and drop off the car at a major rental company office but get a much better rental price.
Many find advantages to drive and sightsee along the way to be a fun thing with a chance to see much more of Austria.
The train ride does not really offer great scenery except that area very near to Salzburg.
Especially with 2 or more traveling together the cost can be equal or better than the train considering the added things available to you-
example a tour through the lake country east of Salzburg, Melk Abbey , the Wachau, Dürnstein etc.
Check out Budget. From the big companies, they seem to be the ones with the lowest rates. We spent two weeks in the Salzburg area two years ago, and we are going back again this August. We went from Vienna to Salzburg (and back) by car and it is definitely worth it, plus it is cheaper if you are a party of two or more. There are a lot of nice places you can stop on the way, somebody already mentioned Melk. I would add Steyr, even though it's a bit off the highway it is definitely worth it. It's a nice little medieval city.
Two years ago, we booked our car from Carhire3000.com who gave us a car from Budget. Actually we didn't know where the car was from until we arrived at the airport and looked for the place written on the voucher. This year, I went to book with them again and out of curiosity I also checked Budget themselves. Well now the official Budget prices are about the same (even a bit cheaper)!
for what it's worth, I find that renting in Germany is always cheaper than in Austria. Usually significantly so. I have been doing this annually for over 25 years, always the best offer I could find. If anyone arrives in Munich, that's where I would rent. From there to the Austrian border is less than two hours by car at a leisurely speed.
Have gone through gemut twice and received great rates and service. On their website they used to have a piece about renting in Germany vs other countries and it does back up what the previous poster said about rates being cheaper in Germany but if you have to drop the car in Austria you would probably be better off to rent in Salzburg and avoid the drop off fee to another country. You could call the toll free number and ask Andy or Bob Bestor for the best advice.
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