Ben Futcher's debut as the new manager didn't go as smoothly as hoped, as Ballymena put up a tough fight against his team. Lee Carsley had moved up to the senior squad, leaving Futcher in charge for the first time, but despite his efforts, the hosts proved to be a formidable opponent.
Reigning champions England were already playing catch-up after losing to Ukraine earlier in the qualifying campaign and may now have to settle for a play-off spot.
Futcher was forced to make changes after losing a number of his initial squad - including Liverpool's Harvey Elliott and Adam Wharton of Crystal Palace - and England struggled to break down a packed Northern Ireland defence.
Manchester City's James McAtee, the standout talent on show, forced Pierce Charles into a first save after 25 minutes with a smart turn and shot that took a deflection.
TrendingCharles was then out well to deny Jonathan Rowe after he was played in by Elliot Anderson, while there was a long stoppage for treatment to England goalkeeper James Trafford following a late challenge from JJ McKiernan.
Trafford was able to continue but the frustration continued for the visitors, with Morgan Rogers heading over from a free-kick.
McAtee began the second half by drawing another save out of Charles at his near post, however, clear-cut chances were few and far between and the hosts began to look more of a threat.
Substitute Makenzie Kirk shot over in the 76th minute and, after Charles produced another fine save to deny Anderson, Justin Devenny nearly won it for Northern Ireland with a spectacular long-range volley that flew just over the crossbar.
England will host Austria in a friendly at Kenilworth Road on Monday, while Northern Ireland play Ukraine on Tuesday.