Glenn Houston, who was the only original panel member, cited personal reasons for his departure.
He remained on the inquiry team last year after the resignation of the chairwoman, Susan O'Brien QC, and panel member Prof Michael Lamb.
One survivors' group said it was "indicative of a crisis" in the inquiry which is examining allegations of child abuse in residential accommodation.
Andi Lavery, spokesman for the survivors' group White Flowers Alba, said victims were rapidly losing confidence in the inquiry's credibility.
And Alan Draper, from In Care Abuse Survivors, said survivors were "at a loss" to understand what was happening.
He told BBC Scotland: "There is concern that the inquiry is dominated by the legal profession, without any balance from other professional groups who have a detailed knowledge of child abuse and its impact and implications for survivors and their families.
"Survivors are considering withdrawing from this whole process until they are satisfied that survivors are placed at the centre of the inquiry.
"The inquiry is about what happened to them and the failure of the establishment to protect them from harm. This failure is continuing."
The probe is due to report in late 2019.
Mr Houston said a "change in priorities" in his working life meant he had applied for positions at the Northern Health and Social Care Trust and the Disclosure and Barring Service.
"I have now been successful in those applications and the appointments have been made," he said.
"Lady Smith and I have discussed the potential that at some future time, a perception of conflict of interest may arise between these appointments and my work as a panel member on the Scottish Child Abuse Inquiry.
"After careful consideration of both the time commitment required to fulfil these new roles and the potential, however small, for perceptions to arise of conflict of interest, I have tendered my resignation to the inquiry."
Mr Houston added that he had been "honoured" to be appointed to the panel.
Deputy First Minister John Swinney said he had accepted the resignation of Mr Houston and thanked him for his positive contribution.
"I know this was not an easy decision for him to reach, but he can be very proud of the contribution he has made to the establishment of the Child Abuse Inquiry and to ensuring its continuing progress," he said.
In July 2016, senior judge Lady Smith was appointed as the new chairwoman of the inquiry following Ms O'Brien's resignation.
A successor to Mr Houston will not be appointed to the inquiry so Lady Smith will continue as the sole panel member.
The Scottish government said this brought it in line with other public inquiries established in Scotland under the 2005 Inquiries Act.
The abuse inquiry has been plagued by problems since it was set up in October 2015. More than Â£3.5m has been spent on it during this period.
Prof Lamb resigned in June 2016 claiming the inquiry was "doomed".
Ms O'Brien stood down days later after being told she faced the sack over "unacceptable" comments about child sex abuse victims.
The QC complained of government interference in the inquiry which she said had "undermined" her.
But the Scottish government denied it was interfering with the inquiry and Lady Smith has also since insisted the investigation will be fully independent.
Scottish Labour said Mr Swinney needed to reassure survivors the inquiry would not be delayed further and urged him to appoint more panel members.
The party's education spokesman Iain Gray added: "What is important is that the inquiry proceeds promptly so survivors can feel a sense of justice."

9 July 2017 Last updated at 14:27 BST
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