Thorne and two others flew from Perth to Brisbane and Sydney late last year.
Sydney's Central Local court heard the men wanted to avoid the scrutiny of authorities and the media.
Mostafa Shiddiquzzaman, 19, was sentenced with Thorne today on the same charges.
The third man, Omer Issak, was sentenced to community orders in Perth last month.
Magistrate Mark Buscombe said the offences were serious and there was clearly some planning involved.
He took into account the men's ages, but said the sentence would be a deterrent to others. Thorne, 26, will be eligible for parole in December and Shiddiquzzaman in November.
Thorne, who has controversially supported the French Charlie Hebdo terror attack and slain terror suspect Numan Haider, wanted a "new start" in Sydney and was remorseful, his lawyer told a Sydney court last week.
In his sentencing remarks, Magistrate Buscombe said Shiddiquzzaman booked the tickets through Flight Centre on a credit card in his name.
The frequent flyer number on the booking was linked to Thorne but when he called to confirm the flight, he was told it was cancelled.
Thorne re-booked flights for December 8, still under the false names.
Shiddiquzzaman was arrested on December 12 in Perth and when asked why the tickets were bought in false names he replied: "Just for fun, trying it out...just to see if it works and it did".
A month later the AFP raided Thorne's home and seized phones, sim cards and a laptop.
"Mr Thorne said that the flights were booked under false names as Mr Shiddiquzzaman didn't want people to know that he was travelling with him, because of his high profile media identity," Mr Buscombe said.
Thorne's online postings in support of the Charlie Hebdo attack in Paris and Melbourne slain terror suspect Numan Haider have been the source of controversy.
Thorne, who travelled to Sydney from Perth to find employment, admitted his intentions were to "elude authorities" to travel within Australia, the sentencing remarks state.
Mr Buscombe found the most serious aspect of the offending was Thorne and Shiddiquzzaman's reasons for travelling under false names.
"The security services are obviously an important apparatus of government and have as one of their primary objectives the protection of the Commonwealth," he said.
"It is notorious that we are living, regrettably, at a time of heightened security concerns."
Issak, 22, was sentenced in Perth last month and given a 12-month community-based order.
- with AAP
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