Mr Baltzer pipped Martin Lau, China specialist at First State, to claim top spot when the latest investment performance figures for the three years to September 30 were compiled by financial publisher Citywire.
His rise to first position came despite a fall in his UK-wide position from 31st to 36th.
Mr Baltzer replaced Douglas Brodie, manager of the Baillie Gifford British Smaller Companies fund, who fell to fifth spot in the Scottish list.
Its is the fourth time this year Mr Baltzer, who has a mathematics degree from Durham University, has headed the table.
He joined Baillie Gifford after graduating in 2001, and is now an investment manager in the credit team.
Mr Baltzer's £295.2 million High-Yield Bond fund typically holds paper issued by between 40 and 60 companies.
His biggest sector bet is capital goods, which accounted for 14.6% of the fund at the end of September followed by finance and investment at 14.2%.
The Investment Grade Long Bond fund holds a portfolio of investment grade bonds denominated in sterling. Its holdings include paper issued by the likes of Network Rail and Royal Bank of Scotland.
Mr Baltzer is one of 16 Baillie Gifford managers to feature in the latest Scottish top flight, up from 12 last month.
The venerable investment house saw head of global income Dominic Neary as well as joint senior partner Charles Plowden and his co-managers on the Global Alpha Growth fund Malcolm MacColl and Spencer Adair added to the ranks of top managers.
Mr Lau runs First State's £510m Greater China Growth fund. At the moment its biggest weighting, at 31.6% is towards the financial services sector. Just over half the fund is in mainland listed stocks. He was ahead of fellow Asia specialist, Hugh Young of Aberdeen Asset Management.
Mr Young co-founded Aberdeen Asset Management Asia in 1992 and oversees funds ranging from broad Asia Pacific mandates to those specifically targeting Chinese and Indian equities.
The Citywire rankings are based on risk-adjusted performance against relevant benchmarks. Fewer than one-fifth of fund managers in the UK qualify for a Citywire rating of which there were 289 in the period.
The Herald-Citywire survey covers fund managers working for investment houses with a significant presence in Scotland.