Edinburgh was ranked third overall for competitiveness while Aberdeen managed 12th position, but Glasgow ranked only 33rd, well down the field of 74, with Dundee 38th.
The study at Birmingham University attempted to measure five areas – enterprise, talent, connectivity, costs and wellbeing.
The top two places were awarded to Cambridge and Oxford.
Edinburgh was found to have the "best level of broadband capability (joint 1st) and a very talented workforce (9th overall)".
The capital also scored well on sectoral specialisation, seen as a driver of job creation, and "business churn". The latter effectively means on average, it is losing fewer businesses than other towns and cities in the UK.
The research showed Aberdeen has high levels of satisfied people working in the city's businesses, and high private-sector employment density. It also had a positive rate of churn.
Survey author Professor Francis Greene said: "This report utilises an extensive range of official data to build a unique picture of the UK, examining the business building blocks that help make a town more or less business competitive.
"It demonstrates the conditions for businesses vary from town to town and these can have an impact on a business's development."
The lowest score in Scotland was 61st, Glasgow's ranking for enterprise, though the city did score better on costs than the other places in Scotland, ranking 20th overall.
On wellbeing, Edinburgh came 22nd, Glasgow 25th and Dundee 27th.