The regulator and STM had been at loggerheads after the regulator sought to appoint inspectors with extra powers to probe perceived failings.
The deal means a court bid to block the inspectors scheduled for 22 January, will no longer take place.
Chief executive Alan Kentish described the deal as a “workable solution”.
In a statement, he said it was “pleasing” they had avoided a court date which was in “neither party’s interest”.
A spokesperson for the GFSC said: “It has been important for both parties to work together to reach a satisfactory agreement. This can take time given the detail that has needed to be worked out and agreed, and is a good outcome.
“The agreed scope for the skilled persons review remains unchanged from the scope for the inspectors’ review.
“What is important and beneficial is that we have reached an agreement and we can move ahead with our work.”
Skilled person review
The scope of the Deloitte investigation will cover the effectiveness and oversight of the company’s internal compliance function and assess any potential conflicts of interest arising across the business.
The review will also cover pensions and life assurance business relating to take-on and monitoring procedures for intermediaries, clients and investments advised by intermediaries.
The Deloitte auditors will report their findings to STM and the GFSC at the end of March.
STM also said it would produce a trading statement on 24 January.
Separately, Kentish and one other STM employee is still subject to a Gibraltar Police Money Laundering Unit investigation.