Spurs had reservations about their star striker going to the tournament in the Czech Republic after a long season, but coach Gareth Southgate named him among a 27-man party at a press conference on Wednesday.
Manchester United left-back Luke Shaw has been left out of the squad which will be reduced to 23 players for the tournament.
Manchester United boss Louis van Gaal said Shaw needed to rest this summer after an injury-plagued season, and the Red Devils full-back was left out of Southgate's party for the tournament.
Kane's situation is complicated by the fact that Spurs play a friendly in Malaysia on May 27 and in Sydney three days later.
The Under-21 squad is due to meet in early June, but Kane will join up later on.
Everton defender John Stones is included in the squad for the tournament, which takes place in the Czech Republic from June 17-30.
After scoring 10 goals in 10 Under-21 qualifying appearances, West Brom striker Saido Berahino is also included.
Danny Ings has been picked after scoring 10 goals for Burnley this season.
Senior internationals Ross Barkley, Raheem Sterling and Alex Oxlade-Chamberlain were eligible but have not been selected.
Arsenal's Calum Chambers is the only senior international that has been named in the squad.
Stoke's Jack Butland is named and will be Southgate's number one for the championship.
Tottenham's Eric Dier, Arsenal's Carl Jenkinson and Ruben Loftus-Cheek are other notable inclusions, while Patrick Bamford, Nathan Redmond and Alex Pritchard have been rewarded for their form in the Championship by being included.
The Young Lions qualified for the tournament with an exemplary record.
They dropped two points - and conceded just two goals - in their qualifying group before beating Croatia 4-2 on aggregate in a play-off last October.
They play their first match in the tournament against Portugal on June 18 before taking on Sweden and Italy.
Southgate's team will play a friendly against Belarus on June 11 in Barnsley before departing for the Czech Republic.
Kane has enjoyed a fairytale season, having risen from third-choice striker at his boyhood club to plunder goals aplenty and score 79 seconds into a dream England senior debut.
Southgate praised the 21-year-old and said of his decision to include him in the squad : "He's had a fantastic season first and foremost and he's been a big part of our team and I think that's important for all of the group.
"(It's) a great stage for Harry to show people his ability on the international stage in a top tournament and good for his development, and good for the group so we're able to take as strong a squad as we can."
On his relationship with Tottenham, Southgate confirmed that the Premier League club support his decision, adding: "Tottenham are one of our best clubs - in terms of all of the age groups - that we work with.
"A tremendous number of our good young players at every level work at Spurs and I've got a really good relationship with Mauricio (Pochettino).
"Always at this moment, if you say to any club 'would you prefer that the player didn't go away all summer and play?', I'm sure all 16-17 clubs would say 'ideally not' but you agree that in the end we'd like to take the best players to the tournament and give them that experience.
"I think that's been the basis of the discussion that we had and we're grateful for their support, as we are with all of the other clubs."