The academy graduate was one of several half-time changes for Burnley and made an impact inside the final 20 minutes by coolly curling home after good work from Scott Arfield.
Gilchrist, who scored a hat-trick at Old Trafford in an FA Youth Cup win over Manchester United in 2012, made it two goals in as many games, his strike sealing Burnley's second friendly win in succession.
Sean Dyche's men thrashed Austrian outfit Grossklein 8-0 last Sunday, but the meeting with neighbours Accrington provided a sterner test for the Premier League newcomers.
Stanley's Josh Windass had the first effort of note in the third minute, bringing a smart low save out of Matt Gilks.
Danny Ings, Burnley's top scorer in all competitions last season, thought he had put his side ahead in the 23rd minute after tucking home a rebound from Dean Marney's parried effort, but the flag was raised for offside.
Ings was involved again three minutes later, setting up Marvin Sordell, but his fellow striker's volley flew narrowly wide.
Dyche fielded a much-changed side after the interval but the visitors continued to press and got their reward with 17 minutes remaining, Gilchrist the beneficiary of Arfield's endeavour down the right as he swept in the winner.
Windass remained a threat, bringing a save out of Alex Cisak from long distance in the 79th minute, but the hosts were unable to force an equaliser as Burnley held on to secure success.
