Saint-Etienne turned the left-back’s loan from Everton into a permanent deal earlier in the transfer window following his performances in Ligue 2 last season.
However, Nkounkou has not been keen to spend one more season in the second tier of French football.
A move to Eintracht Frankfurt has been brewing for the last few weeks and a deal is finally in place for the move to happen on deadline day.
According to French radio station RMC, Saint-Etienne are set to receive a fee of €10.5m from the left-back’s departure.
The deal is also set to benefit Everton who inserted a sell-on clause in the agreement that saw Nkounkou move to Saint-Etienne.
Everton had a 30 per cent sell-on in the deal and are now due a significant pay out from the defender’s move to Eintracht Frankfurt.
Nkounkou has also agreed to sign a five-year deal with Eintracht Frankfurt and will play in the Bundesliga this season.