Toby Fisher, one of the first three barristers appointed to the inquiry, said he wanted to stand down in August.
It is understood he was concerned by the inquiry's "progress and direction" and was not otherwise planning on leaving.
A spokesman for the inquiry would not comment on specifics and Mr Fisher declined to comment.
Mr Fisher had served as first junior counsel - the joint-second most senior barrister on the inquiry - and previously worked on two of the inquiry's most high profile investigations - into Lord Janner and alleged abuse in Westminster.
He notified the inquiry of his intention to step down more than two months ago.
Mr Fisher's decision to leave came about a fortnight after the departure of the inquiry's third chair, Dame Lowell Goddard and days after Newsnight disclosed the inquiry had been told of an alleged sexual assault by the inquiry's lead counsel, Ben Emmerson QC.
The alleged victim did not wish to complain about her claim that Mr Emmerson groped her in a lift, but the inquiry has been criticised for failing to investigate wider concerns about Mr Emmerson's behaviour and for allowing him to step down but continue working for two months on Â£1,700 per day.
The BBC understands that Matrix, the set of chambers to which Mr Emmerson belongs, has launched its own independent inquiry into the allegations, to be carried out by an external figure.
Mr Emmerson categorically denies sexual assault, bullying or other misconduct.
The inquiry has denied that either Prof Alexis Jay, who was appointed in August as the fourth head of the child sex abuse inquiry, or the panel received any complaint about an alleged sexual assault, however they have declined to comment on whether an alleged incident was disclosed to them.
'Stop knocking inquiry'
On Monday, Labour MP Lisa Nandy asked Home Secretary Amber Rudd about the inquiry's handling of the disclosure of the alleged sexual assault.
Ms Rudd said it was a question for the head of the independent inquiry, adding: "I would urge [Ms Nandy] to stop knocking the inquiry and get behind it."
The troubled inquiry, launched by Theresa May when she was home secretary, has already seen the departure of three chairs as well as its most senior and second-ranking counsel.
Asked about Mr Fisher's departure, a spokesman for the Independent Inquiry into Child Sexual Abuse said the inquiry had "a large legal team comprising a number of junior counsel, senior counsel and solicitors".
"They come and go subject to their professional obligations and we are not commenting on specifics," he added.
The spokesman for the inquiry added that Toby Fisher remains instructed by the inquiry. However, the BBC understands that this is to allow Mr Fisher to answer any queries that arise related to his previous work.
A key lawyer for the independent inquiry into child sexual abuse has resigned, BBC Newsnight has learned.