Heriot-Watt University, in Edinburgh, came top in Scotland and 52nd overall after rising from 63rd place last year.
Heriot-Watt has overtaken Stirling University in the rankings, which now stands at 56th after rising from joint 61st.
Strathclyde University, in Glasgow, the country's only other top 100 institution in the Times Higher Education magazine table, rose one place to 78th.
The rise in the rankings comes at a time when Heriot-Watt has been widely recognised as one of the most successful international institutions.
The university attracts a large proportion of international students to its campus and also delivers degree programmes to 11,800 students in 150 countries around the world.
A spokeswoman for Heriot-Watt said: "We are delighted at this news and that we have improved on our position from last year. "