After what the firm called “an outstanding career with both the company and earlier with Aberdeen Asset Management”, Mr Gilbert has said he will not seek re-election at the company's Annual General Meeting, scheduled for 12 May.
He will retire from the firm on 30 September.
Sir Douglas Flint, chairman, said: "It is impossible to overstate Martin's achievement in building Aberdeen Asset Management into a truly global and widely respected investment firm.
“His ability to attract talent to deliver that success and his unrelenting commitment to the firm's clients leave a legacy of which he should be immensely proud and which serves as a solid foundation for our future success.
“His foresight to see the opportunities that led to the combination that created Standard Life Aberdeen and his tireless efforts to realise these opportunities post-merger are hugely valued by all his colleagues who now take up the responsibility to deliver on them.
“On behalf of the Board and fellow shareholders, I would like to thank Martin for his dedicated service and contributions to Standard Life Aberdeen, particularly as it came together after our merger in August 2017.”
Mr Gilbert, said: "It has been an incredible journey, almost unimaginable from the earliest days when we were just three people in one office in Aberdeen with £50m under management to today's total in excess of £500bn.
“For more than 30 years, I have been fortunate to have worked with brilliant people all across the company, and I would like to take this opportunity to thank all my colleagues - past and present - who have supported me on this journey.
“I will leave the company in extremely good hands, and well-positioned for further growth and prosperity.
“I am very proud of our achievements over the past three decades, but I still have a great enthusiasm for growing and guiding businesses and I am looking forward to fresh challenges in the next stage of my career.
“Nevertheless, Standard Life Aberdeen will always be close to my heart, and I wish everyone associated with the company all the very best for the future.”