Flynn, who was appointed after the Welsh club sacked boss Graham Westley on March 8, has won both his matches in charge so far.
And the morning after Tuesday's 1-0 victory at Morecambe, the 36-year-old received a congratulatory text from former Arsenal striker Henry.
The two are both studying for their coaching badges and are on the same course run by the Welsh FA, following in the footsteps of former graduates Roberto Martinez, Garry Monk and Tim Sherwood.
"It was surreal," said Flynn. "He's one of my heroes in the game. He's just pure class and he's like that off the pitch as well.
"I asked him to put his boots back on, but he wasn't so forthcoming.
"For a football fan it was unbelievable, and something which made me smile on Wednesday morning when I had my little boy waking me up at 6.30 in the morning, after getting back from the game at 4am."
Newport are now seven points from safety and have 10 games left of the season to play.
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