He will be replaced by Stephen Bird, who was previously chief executive at Citigroup’s global consumer banking arm from 2015 to last November.
Bird has had various senior management roles at the bank over the course of 21 years.
His salary will be £875,000 per annum, with an annual bonus of up to 250% of salary subject to performance.
Skeoch is announcing his departure two months after vice-chairman Martin Gilbert left the company, which was formed from the merger between Aberdeen Asset Management and Standard Life in 2017.
Skeoch and Gilbert, who came from the two separate sides of the business, served as co-chief executives until last year, when Gilbert took the chairman role as shareholders did not like the split leadership.
Shares rose 3% to 275p on Tuesday morning.