Christopher Chisholm, 31, is accused of acting in a racially aggravated manner towards the SNP politician.
It is alleged that Mr Chisholm, from Gartcosh, shouted and made racist remarks on 7 February outside Queen Street station.
A not guilty plea was entered on his behalf at Glasgow Sheriff Court and a trial was set for May next year.
Mr Yousaf, 29, was elected in 2011 as a SNP member of the Scottish Parliament for Glasgow.
Since September 2012, he has been Minister for External Affairs and International Development.
A man will stand trial next year for allegedly making racist remarks to Humza Yousaf MSP.