The Japan international has put pen to paper on a contract that commits him to the Italian club for another three years
The left-back first joined the Nerazzurri on loan from Cesena at the start of 2011 before moving permanently in June of the same year.
"FC Internazionale is pleased to announce that Yuto Nagatomo has signed a contract extension with the club," Inter announced on their official site.
“All the paperwork relating to the Japanese defender's new deal, which runs until June 2016, has been completed.”
Nagatomo became the club's first ever Japanese player upon his arrival and has 54 caps to his name.
Inter return to Serie A action on Sunday when they take on Udinese, but the defender will be missing through injury.