Gareth Southgate names his provisional squad for the tournament in the Czech Republic on Wednesday and if Kane is included, it will leave the striker only 18 days to recuperate after Tottenham’s post-season tour of Malaysia and Australia.
Spurs face Everton on Sunday in their final Premier League fixture of the season before the squad fly out on Monday to face a Malaysia XI in Kuala Lumpur on 27 May and Sydney FC three days later.
That would mean Kane would have less than three weeks’ break before the opening match of the U21 tournament against Portugal on 18 June with the final scheduled for 30 June.
The new Premier League campaign begins on 8 August and Pochettino said: “Could he miss the start of the season? Maybe. But it is because of that I am sure the FA will take the right the decision for Harry Kane and for England.
“I am happy if Harry is happy. In the end, it is a decision for the FA. We need to wait for the FA’s decision.
“If Harry asks me, I will say it is his decision. If you have the possibility to play in the Under-21s, it is always the player’s decision.
“We can advise him but it is up to the FA and the player. The problem is there are different interests. We are a club in England and we need to be careful.
“The manager’s decision in this case is to build the team and decide and pick different players. His decision and our interests are maybe different to the FA’s. But we understand the decision will always be with the FA.
“The problem is when you play a lot of games in the Premier League and Europa League, you spend a lot of energy and it is not easy. He is not tired, it is about next season. We can see him in the future because for us he is a future number one in the senior England squad.”