The 28-year-old midfielder has penned a one-year deal with the Edinburgh-based outfit, having spent the second half of last season with the club on non-contract terms.
He joins on a free after seeing his contract at Middlesbrough cancelled by mutual consent in January.
The Scotland international is delighted to have reached an agreement with a club that means so much to him - as he graduated out of Hibs' academy system at the start of his senior career.
He admits he had other options to consider south of the border, but claims the opportunity to remain true to his roots was too good to turn down.
Thomson said in the Sunday Mail: "There were offers on the table from clubs down south but I knocked them back because I had my mind set on staying with Hibs."