Two draws and a defeat meant they missed out on a route to the last 16 of the competition and were on their way home earlier than hoped.
But what it did give the Merseyside duo is a taste of World Cup football. Roll the clock forward 12 months and they are enjoying the build-up to Brazil 2014 with Roy Hodgson's senior team.
The defenders, rivals from across Stanley Park but very much friends for their country, are on standby for England and have travelled to Miami for the World Cup warm-up double header against Ecuador and Honduras.
John Stones takes advice from Roy Hodgson during the Liverpool man's debut
And it is something they never imagined would have happened so soon.
Flanagan admitted: "We didn't fulfil out potential at the U20s World Cup.”
Stones added: "For me and Flano to get in that World Cup squad was a massive achievement. I think we were upset when we got knocked out so early.
"But a year on where we are now, we never would have thought it would have happened so quickly, coming away with the senior squad.
"We're just enjoying every minute of it. It's nice to see how the senior squad works - it's all good experience."
Flanagan, who is in the setup alongside five other Liverpool players as well as new signing Rickie Lambert, said: "The difference [between U20s and Seniors] is massive. It's a lot quicker and everything about it is more professional.
"There's a lot of Liverpool players in the squad and it helps you out massively. There are also a lot of young lads in the squad who we have played with down the years, so it helps you when you are coming into the squad and makes you feel welcome."
Jon Flanagan has benefited by being around Liverpool team-mates, including Daniel Sturridge
For Stones, his welcome into the squad could not have ended any better. Having turned 20 two days earlier, he added to his 26 first-team appearances with Everton this season by winning an England debut against Peru at Wembley last Friday.
And though the pair are heading home when the team flies to Brazil, Stones says he has only become more hungry for international recognition in the future.
"It's still not sunk in yet," he said, "I'll never forget that moment at Wembley and it still feels surreal.
"To make my debut two days after my birthday as well topped off the week. It was nice to have the family down and it was a massive day for me."
Flanagan chipped in: "He handled his own. I thought he did well, got forward and it was a debut to remember.
"As we've seen, young players are getting their chance and those who have come in have taken it with both hands. If I get a chance then hopefully I can take it."
Stones continued: "It's been really good [in Miami] so far. It's been humid and we're just trying to get acclimatised.
"The first day was not what we expected - it was banging it down with rain and we had to adapt our training session a bit.
“It's still not sunk in yet. I'll never forget that moment at Wembley and it still feels surreal”
John Stones on his England debut
"It's been such a good experience, we'll go away and watch the lads from back home.
"But it has given us that hunger to keep on improving and hopefully when that next England squad comes around we'll get the call."
Before Stones and Flanagan head home, though, England have two games at Sun Life Stadium against Ecuador on Wednesday and Honduras on Saturday. And while Stones already has his first senior cap, Flanagan hopes he can get his chance too.
"Coming away with your country, it doesn't get much better than that," he said, "There are top players from all around the country, so training with them is really good.
"There are another two games before we go home so if I get the chance [to make my debut] it will be a dream come true."
Stones added: "These are the games we go into and are focusing on ourselves and looking to make improvements to take into the World Cup.
"There are a lot of positive vibes about the camp. All the lads are focused on the job and what they want to achieve and are taking it a step at a time."
