The duo, who both have backgrounds in psychology, run the Baillie Gifford Japanese fund. They saw their UK-wide ranking rise from 45th to 15th when the latest performance figures for the three years to the end of October were compiled by financial publisher Citywire.
Ms Whitley, who moved to Edinburgh when she was 12, rowed for Oxford University where she read experimental psychology.
A sailing enthusiast, her first posting at Baillie Gifford in 1980 saw her working on UK equities alongside Douglas McDougall, later managing partner, and Max Ward, who went on to establish the Independent Investment Trust.
Ms Whitley became a partner at Baillie Gifford in 1986.
She joined the Japanese equities investment team in 1982 and has been heading it since 2001. Her tenure on the £173.2 million Japanese fund dates back to 2004 while Mr Brett became a manager on the portfolio in 2008.
Mr Brett had joined Baillie Gifford's graduate scheme three yeas earlier after taking a PhD in Psychology at Bristol. He had previously graduated in natural sciences from Cambridge University.
The pair's presence at the top of the Scottish leaderboard is notable because the Japanese stock market is notoriously tricky for fund managers to navigate.
It has had a particularly torrid time in recent years as investors worried about its ageing population, large state debt and lacklustre growth.
A territorial dispute with China, which has prompted boycotts on both sides of the East China Sea, has caused further uncertainties.
The top holding in the Baillie Gifford Japanese fund as of the end of October was Hikari Tsushin, which primarily sells electronic devices.
Japan Tobacco is the second largest holding.
Ms Whitley's and Mr Brett's rise to the top came at the expense of perennial table leader Robert Baltzer, who runs the Baillie Gifford High Yield Bond and Baillie Gifford Investment Grade Long Bond funds.
He fell from first to third place and his UK-wide ranking slipped from 31st to 33rd.
The last time a woman headed the list was when SVM Asset Management's Margaret Lawson, who then, as now, was manager on the SVM UK Growth fund, topped the table for August 2010.
That was at the end of a period when she had consistently vied for the number one placing with fellow Edinburgh-based manager and smaller companies expert Elaine Morgan of Aegon Asset Management, which is now called Kames Capital.
The Herald-Citywire survey focuses on open-ended funds aimed at retail investors, and ranks the performance of those working for investment houses which have a significant presence in Scotland.
Fewer than one-fifth of fund managers in the UK qualify for one of the 276 Citywire ratings. Rankings are based on three-year, risk-adjusted performance set against relevant benchmarks.