The Edinburgh club intend to take a slightly different approach to their youth policy from now on and are expected to appoint a new figurehead to run the entire system.
Arnott spent seven and a half years managing the Riccarton development programme after being named academy manager by former director of football Craig Levein in 2014.
He departed his post on Friday and Hearts officials are now considering what type of replacement should be hired.
Sporting director Joe Savage is looking to reorganise after luring John McLaughlan from Celtic last July to become Hearts’ academy coaching development manager.
Tynecastle Park officials see the youth academy as a key area of the club for producing home-grown talent to play in the first team.
Recent graduates of the programme include Euan Henderson, Finlay Pollock and Scott McGill. All three have been on the periphery of the senior squad in recent seasons.
It is understood senior Hearts officials want the academy to produce even more players if possible as the club target a regular challenge near the top of the cinch Premiership.
They also want to qualify for European football regularly and have already overhauled the recruitment system by appointing William Lancefield head of recruitment last July.
At the same time, George Brown arrived from Rangers as lead recruitment analyst. Both men contributed to the signings of first-team players including Cammy Devlin and Nathaniel Atkinson.