A 70 year old man planned to crash two trains and after they crashed he wrote a letter in Arabic and left it the scene to trigger a backlash against the Muslims.
He cut down trees that would fall on railway tracks to cause a collision between trains.
The incident happened in Mlada Boleslav in Prague.
State attorney Marek Bodlak said the defendant left leaflets at the scene “containing linguistically garbled threatening texts to evoke that they were written by a jihadist”.
The 70 year old who cannot be named for legal reasons has been accused of terrorist charges and will be sent to jail for life if found guilty.
Mr Bodlak added “The accused is a native Czech citizen, motivated by the effort to raise concerns among the population about the Muslim migration wave and the commission of terrorist attacks,”
The Czech Republic’s criminal code says attempts to “seriously intimidate the population” can be classed as such.
No one was injured in the crash but still triggered a wave of islamophobia and xenophobia on social media.
Martin Konvicka, a high profile anti-Islamic activist in the Czech Republic, reportedly blamed Muslims for the attack, failing to mention the suspicious nature of the messages, which had been transliterated into Latin.