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Is this sentence correct?

Master thesis to obtain the degree Master of Science

I am really not sure about the 's here.

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As suggested by snailplane, corpus searches are a good way to get a handle on which one is preferred.

  • Google Books Ngram Viewer prefers master's thesis by a roughly six to one margin at the year 2000.
  • The Corpus of Contemporary American English prefers master's thesis (212 to 6).
  • The Corpus of Global Web Based English prefers master's thesis (384 to 82). Sorry, no direct query links here, since the site uses iframes and I'm too lazy to dig the URLs out. Search master 's thesis (note the space before the apostrophe) and master thesis. This one is a nice corpus because it breaks usages up by country.
  • The Time Magazine Corpus prefers master's thesis 23 to 0 (same search guidelines as above).

I also searched many an exclusively British corpus, but without yielding any meaningful results.

The relevant ELU question that choster linked discusses master's degree, which has the same form as master's thesis. The question is about apostrophe usage, but note that nobody suggested it should be master degree.

Grammatically speaking, master's thesis unequivocally means a thesis of a master. Master thesis can be read the same way, but also as primary, principle or main thesis.

Stick with master's thesis.

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    It seems like every single chair of my (German) university's CS department uses Master thesis and it's making me question my sanity -- thanks for this. – user134593 Sep 26 '18 at 11:14

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