"She has been suffering from shingles and medical advice has suggested resigning was the best course of action.''
Deputy chief of staff Karl Beckett was filling the role in her absence and a process to find a replacement was underway.
"Labour wishes to thank her for her great work in getting the office set up and wishes her a speedy recovery.''
Ms Brandon was appointed after Mr Cunliffe took over the leadership. Former leader David Shearer's chief of staff Fran Mold left after Mr Shearer resigned.
Ms Brandon was General Counsel at Auckland Council before entering Mr Cunliffe's office and was seconded as a senior adviser when he was Minister of Health.