The defender was not included in England's squad for their remaining Euro 2024 qualifying games, with Gareth Southgate saying James' spot for next summer's tournament is at risk.
The 23-year-old has struggled with injury throughout this season so far.
"It is not a decision by him, he is desperate to go," Pochettino said.
James has started just two Premier League matches this season after injuring his hamstring.
He has played just one game for England - against Italy in March - since being ruled out of last winter's World Cup in Qatar.
It is understood Chelsea's medical staff are being careful with James as he continues his journey to full fitness and his minutes and recovery are being managed.
"It's never the decision of the player in these cases; it's about assessing. The medical, sport science, and coaching staff take the decisions and not the players," Pochettino said.
"I think it is good the communication between the national team and club to make the best decision for both.
"It is not the decision of Reece, he is desperate to go, he wanted to go. But there are two parts between the national team and club to take the best decision for him."
Pochettino also said he "respected" Southgate's decision to leave Chelsea forward Raheem Sterling out of the England squad.
Sterling has been left out of five successive England squads, but Pochettino said: "I don't want to say nothing that goes against the decision of my colleague Gareth.
"The only way to change the situation is by working hard in your club and showing you deserve to be involved."
Chelsea play league leaders Manchester City on Sunday at Stamford Bridge and Pochettino says he will never accept that his side are the underdogs.
"For me, they [Man City] are the best team, have the best coaching staff and the best coach-manager. We need to tell the truth - it is one of the best organisations in the world," Pochettino added.
"We need to give credit to Manchester City, from the top to the bottom, they are doing it all well.
"It is going to be a challenge and we want to compete. We know it is going to be tough. But we are going to try to compete at our best and our goal is to win the three points.
"Chelsea never have that feeling of being an underdog. The feeling is always 'you are Chelsea'. It is impossible, the history is there.
"But Monday [against Tottenham] we showed we have talent and character to compete and to fight with the best clubs in England".
