The 500 billion pound ($613 billion) fund firm said former co-chief executive Gilbert, currently vice-chairman, would not seek re-election to the board at its annual meeting in May and would leave in September.
Gilbert oversaw the meteoric rise of Aberdeen Asset Management, the small company he co-founded in 1983 with just 50 million pounds in assets, to what became the country's biggest listed fund firm at the time of its 11 billion pound merger with Standard Life in 2017.
Touted as a strong tie-up of two of Scotland's biggest financial services companies, Gilbert and Standard Life peer Keith Skeoch initially shared the role of chief executive, despite some discontent from shareholders.
The unusual arrangement became a deeper problem, though, as persistent share price underperformance on the back of heavy outflows of client cash and broader corporate upheaval linked to the merger drew calls for change.
Former HSBC Chairman Douglas Flint was drafted in to lead the board and in March this year Gilbert stepped down from his role as co-CEO to become vice chairman.
"It has been an incredible journey, almost unimaginable from the earliest days when we were just three people in one office in Aberdeen," Gilbert said. "I will leave the company in extremely good hands, and well positioned for further growth and prosperity."
At 0724 GMT, shares in SLA were down 1.4%, slightly underperforming a 1% fall in the FTSE 100 <.FTSE>.
Until his departure, SLA said Gilbert would continue to focus on strengthening relationships with clients, winning new business and realising the potential of its global network.
His key client, industry and regulatory relationships would be transferred to Flint and other executives.
The 64-year-old golf fan said he still harboured "a great enthusiasm for growing and guiding businesses" and was looking forward to "fresh challenges" in the next stage of his career.
The Financial Times reported in July that Gilbert was in line to take up a role as chairman of digital bank Revolut.
The bank declined to comment on Wednesday.
($1 = 0.8156 pounds)
(Reporting By Sinead Cruise; editing by Simon Jessop and David Evans)
By Sinead Cruise and Simon Jessop
