DVD?

you can generally get it on ebay as both the english-dubbed version
(from laserdisc originally probably) - sound & image is quite reasonable,

& from a visually top-notch Japanese release although this has no subs or dubs, being the original Czech language only (also top-notch).

Alternatively try Amazon Japan where the fairly recent release
(circa 2005 probably ) may still be available
( this has optional Japanese subs & is czech language of course ).
This version was first released as a boxset with Invention Of Destruction (aka Fab. World Of J. Verne )
- that's the version I have -
but it may have been released separately a bit later perhaps ( or not )

Only thing is; I'm a bit suprised you haven't found it already as the ebay ones were certainly regularly & easily available until recently ( & perhaps still are ):
Ebay being one of the 1st places to look

In dvdgo.com, a Spanish site, you can find a 4-dvd box comprising this film, the Journey into Prehistory, the Invention of the Devil and The Stolen Airship, all in czech with spanish subtitles. As extras you get the short czech dpcumentary of 1980 "Karel Zeman for children" and the shorts King Lavra and Inspiration

It's now out on what hopefully should be a quality DVD & which apparently has good English subtitles
( ie not like the appallingly brief ones on the German release! ) :
The DVD transfer & subtitles were supervised by KZ's daughter Ludmilla.

It's available worldwide now from the Czech Republic's new 'Karel Zeman Museum'.
Their site is www.MuzeumKarlaZemana.cz.
(also see my longer posting here at the film's imdb message board for some more detail -
all of which will be on their site & / or their facebook page. )

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here is the most cheap and quality copy I found http://czechmovie.com/d/baron-prasil-the-fabulous-baron-munchausen-dvd-1000103/

also on amazon is the same copy available http://www.amazon.com/Baron-Prasil-Fabulous-Munchausen-sleeve/dp/B00B4R9K0Y/ref=sr_1_1?ie=UTF8&qid=1440144487&sr=8-1&keywords=baron+prasil