The agreement stipulates that players selected by coach Bernard Laporte will be released from club duties for seven weeks during the Six Nations tournament, as well as for four-and-a-half months ahead of the World Cup, which will be held in France.
In return, the FFR will give 12million euros (Â£8.3m) to the LNR, who will then redistribute the money to their clubs.
The decision comes after months of debate and negotiations between the two organisations.
"This is a unique agreement in the history of rugby which gathers everything around one single project, the World Cup," said FFR president Bernard Lapasset.
Former France international Serge Blanco, currently LNR president, was also satisfied to have finally reached an agreement.
"We had to agree on the schedule, as well as on the financial and judicial sides," he added.
"We had to defend and protect everyone's interests, and everyone is happy."
France, who won this year's Six Nations, won both their June Test matches against Romania and South Africa.
They will resume international action in November with Tests against New Zealand and Argentina.