FA's director of development feels that the two England Under-21 stars will not get much playing time in the first-team at their new clubs, and their progress may be hindered
Henderson completed his reported £20 million move from Sunderland to Liverpool on Thursday, while Blackburn Rovers defender Jones is set to join Manchester United after undergoing a medical on Wednesday.
Brooking feels that the two players may not gain as much time in the first-team at their new teams, given the level of squad depth at Liverpool and Manchester United.
He told BBC Sport: "There is going to be competition for places, with anything like that will they get regular first-team football?
"Let's wait and see and we wish them well."
He added: "Phil is one we think could be challenging to get into the seniors like Jordan has already done.
"The fees put a bit of pressure on them but of course, like any young English player, we would like them to get regular first-team football so we hope they are going to play regularly.
"At Blackburn and Sunderland they were playing every week when they were fit and that's really important for their development.
"It is a challenge. You look at Manchester United and you have Phil Jones going there, you've also got Chris Smalling who is trying to battle away to try and get in the side.
"He's had a couple of games at right-back but again our two [England Under-21] central defenders will now be at Manchester United."
Brooking’s view is similar to that of England Under-21s manager Stuart Pearce, who feels that the most talented young players will not gain enough first-team experience at club level.