The man felled trees by two different railways near the central city of Mlada Boleslav in early June and late July 2017, the lidovky.cz news site said, quoting a prosecutor.
Trains crashed into both trees but no one was injured.
In both places, the man left leaflets with messages in Arabic transliterated into Roman characters.
Police arrested the man last week.
"The culprit is a Czech-born citizen whose motivation was to raise fears of the Muslim migrant wave and terror attacks," the website quoted Prague prosecutor Marek Bodlak as saying.
If convicted, the alleged fake militant faces up to life in prison, said lidovky.cz.
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