Miley, who turned 18 last week, led The Young Magpies to victory with strikes from Callum McNally, Michael Ndiweni and an own goal putting the hosts 3-2 up before two late goals from Colchester saw the match end 3-2.
Miley’s younger brother Lewis also came off the bench during the match to help Peter Ramage’s side set up a fifth round tie at Blackpool.
“It was a good win from the lads and progressing in the Youth Cup is something we aspired towards at the start of the season,” he said following the match.
“It's going well and we've been clinical at the top end of the pitch we just need to tighten up at the back and stop the last goals conceded and a bit of worry at the end but it's all good.
"Afterwards, all the lads were hugging each other after that and celebrating together which just shows how much it means.”
The Gateshead-born midfielder helped Newcastle reach the quarter-final of the FA Youth Cup last season, playing twice behind closed doors at St James’s Park in wins over Leeds United and Watford in the fourth and fifth rounds respectively.
But playing in front of a 1,279 crowd at St James’s on Monday night was a new highlight for the 18-year-old.
“The early goal made everyone a bit more confident and comfortable in the game where we were able to move the ball around a bit more which was good.
“But getting into the next round with a trip away to Blackpool is something we're all looking forward to.”
No set date has been made for the fifth round tie but the FA website states it must be scheduled to take place no later than Saturday, February 5.
A place in the quarter final will be the reward for the winner.