If you want to travel during the day then the best option is to take a train from Katowice. It departs at 11:12 and arrives in Prague at 16:39. It's easy to get from Krakow to Katowice, train travel takes 2hr15 and bus travel about 1hr20.
If prices quoted by Polrail are too high for you then you can travel some other way, less comfortable but cheaper. From Krakow to Cieszyn by bus (3 hrs), in Cieszyn cross the boarder to Cesky Tesin (from Polish side of the town to Czech side) and from there go by train to Prague (3 hrs). It should cost less than 25 euro altogether.
Check buses from Kraków to Cieszyn here: http://en.e-podroznik.pl/Edited: 20 August 2013, 17:02
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