It can be pronounced either way. I prefer the first one, but you will hear both pronunciations from native speakers. Most dictionaries place the middle syllable in parentheses to indicate that it's optional. \ˈmis-t(ə-)rē\

It is pronounced almost the same way as "history"

By native speakers, it is pronounced both ways. Also, I have heard the word, history, being pronounced as [hɪstəri] and as [hɪstri] by native speakers of English.