The defenders were both named on standby for this summer's trip to Brazil by Roy Hodgson and are the only two players from that list of seven who will meet up on Monday with the 23-man squad.
It’s been a quick rise to prominence for Everton’s Stones and Liverpool’s Flanagan who, along with Ross Barkley, were part of the England squad which played in the U20 World Cup in Turkey last summer.
And with Hodgson’s only current injury doubt in the squad being with Manchester United’s Phil Jones, it was seen by the Three Lions boss as a good opportunity to bring the pair into the group for both the experience and as potential replacements.
"I will be taking John Stones and Jon Flanagan with us on this trip," revealed Hodgson.
"I rely on the doctors and physios at the various clubs and our own doctors and the only one I would say who seriously poses a question is Phil Jones.
"He had his shoulder injury a week ago but everyone tells me, and my research tells me too - I had the same injury with two of my players at Fulham - everything points towards him being back, fit and playing in three weeks.
"But we can't guarantee that and John Stones will be Phil Jones' replacement if, by 2 June, we are not confident Phil Jones will be fit, even though everything tells me he will be."
Both players are already personally well known to Hodgson, with Flanagan playing under him during his spell in charge of Liverpool and Stones making his England Under-21 debut last August when Hodgson took charge of their game against Scotland at Bramall Lane.
The pair have won caps with various England development teams over the last few years before catching the eye with their performances at club level in the second half of the season.
And that has given Hodgson more than enough confidence to know both players are more than comfortable with stepping into the senior squad for a World Cup.
"There are some younger players here, but we have worked with them all at one stage or another and we have done our research with the clubs," explained Hodgson.
"We wouldn't have selected anyone in this 23 if we seriously thought we were going to be on tenterhooks with regards to his fitness.
"I hope we will not let anyone down, that we will give a very good account of ourselves, and that the comportment of the players throughout will be 100 per cent professional."
After their trip to Portugal, the England squad will return to play their final match on home soil against Peru at Wembley. Tickets are still on sale for this game, click here for more details.