The University of Edinburgh regained its place in the top 20 after dropping four places in 2018, while Edinburgh Napier and Queen Margaret also moved up the rankings, according to the data released by the Complete University Guide.
The standings - which rank more than 120 higher education centres - are based on ten measures, ranging from entry standards and student satisfaction to research quality and graduate prospects.
Heriot Watt retained its place in 35th from the previous year, ranking above Queen’s University in Belfast for 2020, while the University of Edinburgh climbed to 16th from 23rd after falling from 19th in the previous rankings - its highest position since 2013.
However, Edinburgh Napier was the biggest mover of the four Capital institutions, leaping 15 places from 101st to 86th.
Queen Margaret University jumped nine places to 68th, the highest position it has occupied in the rankings since 2008.
A spokesman for Edinburgh Napier University said: “We are very pleased to note our improved standing, something which reflects all the hard work of our staff to ensure Edinburgh Napier is a great place for students to build their future.”
Nationally, the survey noted Scotland recorded the highest average entry standards while it also noted a year-on-year rise in graduate prospects.
All league tables are made available online for free.
A spokesman for the University of Edinburgh said: “It is always pleasing to see the University’s performance reflected strongly in league tables. It is a tribute to the hard work of our staff and students.”
A spokeswoman for QMU added: “We are delighted to feature as the top modern university in Scotland in this league table and to have moved up seven places year on year.”
“This success reflects our work to provide an excellent student experience in a supportive environment and the quality of our academic research. We look forward to continuing this work.”
St Andrews topped the Scottish rankings, coming third overall across the UK, with Edinburgh second.
Glasgow, Aberdeen and Dundee rounded off the top five Scottish representatives.
Abertay University was the biggest faller in Scotland, dropping four places to 103rd, however Glasgow Caledonian rose from 85th to 77th in the standings.
Universities are also ranked in more than 70 subject categories, as well as student-staff ratios and facilities.
Dr Bernard Kingston, chairman of The Complete University Guide, commented: “The evidence is clear; the increased emphasis, including funding, on employability and career planning within academic departments and student services is bearing fruit.”
“Many institutions now have this as a core element of their strategic plans with the introduction of innovative programmes of subject-specific careers events focussed on embedding and signposting graduate destinations.”