The 27-year-old Frenchman earned a long-term deal after some impressive performances since joining from Brighton in February.
He told the club website: "I'm very pleased to agree this contract. I was on holiday thinking about next season and the choice of my heart was always Orient.
"I feel very at home and comfortable at Orient, we have a terrific group of lads and there's a great atmosphere so the team spirit is excellent. The fans have always made me feel very welcome here too."
Manager Russell Slade added: "Securing the services of Romain is massive for us and I think he will prove to be a top signing.
"He was very impressive when he came into the side later on during last season and though we will predominantly see him as a midfielder, he also showed his versatility when he filled in at centre-back for the last few games.
"He's a great athlete too and gives us plenty of energy."