The Liverpool defender was included in Southgate's Under-21 squad earlier this year, but did not play during their European Championship qualifiers.
However, the Young Lions manager told the Liverpool Echo: "I went to see Jon and Brendan [Rodgers] at Liverpool about a month ago, because I feel he does deserve to be in our squad.
"He's one we'll be looking to involve in the summer, if of course he doesn't force his way into the seniors.
"I know within our Under-21s there are lads that can use the ball, there's no question about that. So for many, it's just a case of being given the opportunity and having a manager and a coach that has belief in them."
Flanagan has made 20 appearances for the Premier League leaders this season.