Anas Abdalla, from Birmingham, has denied preparing for acts of terrorism by hiding in a lorry with another extremist.
He was convicted by a majority of 11 to one and will be sentenced at a later date.
Abdalla, born in Mogadishu in Somalia, who first came to the UK as an asylum seekertold the Old Bailey court that he was fleeing unwarranted security services intrusion in his life.
"It is eminently preferable and in the interests of justice [if the law allows] for the jury to hear the evidence so that they may be in the best possible informed position so as to be able to reach a conclusion that is fair to both the prosecution and the defence in so far as this critical aspect of the case is concerned," Judge Richard Marks said in reference to holding the trial in secret.
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The prosecution had originally scheduled a three-week case at the Old Bailey but took 18 months to complete.
Abdalla has been eventually convicted after the prosecution won a legal battle to take part of the trial behind closed doors.
Abdalla had alleged he was fleeing Britain because he was being "harassed and subject to oppressive treatment" by MI5.
When Abdalla was discovered in the back of a lorry, he was hiding with three other men. One of the other men detained, 29-year-old Gabriel Rasmus, has already pleaded guilty.