Spurs boss Mauricio Pochettino admitted he would rather Sessegnon did not travel for the European Championship qualifier against Albania on Friday and next week's friendly in Holland.
Boothroyd held talks with Spurs' medical team before recalling the 19-year-old, who has only recently returned from a hamstring injury.
"It's a trust situation," Boothroyd said. "He is a big player for us, so we work together, make sure we get him fit and keep him fit.
"The trick is to be open and honest. We look after them. The fact he is 19 and pushing hard to get into the Under 21s team shows how much I value him."
England will manage Sessegnon's workload carefully but will not let Spurs dictate his game time. Boothroyd said: "I don't ask managers how long I should play players. I've been around long enough to know that."