Scotland's reputation as a "welcoming and friendly" is now being undermined over the treatment faced by many of the 223,000 EU citizens living in the country, according to the report by Robert Gordon University.
It raises concerns about the impact on the mental health of EU citizens north of the border and calls for action to tackle this at a national and local level.
Scottish Government Europe minister Ben Macpherson admitted the findings are "hard to hear" but put the uncertainty down to UK Government policies on residency status and other rights.
The report, entitled How Brexit Impacts EU Citizens’ Mental Health And Wellbeing Research Findings, finds the political divisions in recent years have had a stark impact on EU citizens.
"The Brexit campaign, referendum, and subsequent political discourse have damaged EU citizens’ wellbeing primarily through undermining their integration into Scottish society," its states
"They have been left feeling unwanted, unwelcome, marked out as different and treated as inferior. They are concerned with the uncertainty around Brexit, reducing their ability to visualise their future in Scotland.
"Most saw Scotland and the UK as open, welcoming countries before the 2016 referendum, increasing their sense of shock and loss."
It adds: "For some, this rejection materialised as an increase in discrimination."
About 223,000 live in Scotland, making up 4.2% of the Scottish population. Roughly half of all EU citizens in Scotland are Polish or Irish.
Mr Macpherson said: “It is hard to hear that the EU citizens in this study have been left feeling unwanted and unwelcome as a result of Brexit, and because of the UK Government’s policies regarding their residency status and other rights.
“It is clear that the real impact of Brexit is being felt by people on a personal level across the country, and none more so than EU citizens who have done us the honour of making Scotland their home. That is why we have launched the Stay in Scotland campaign, to encourage and support EU citizens to stay here. We will continue to do all we can to support EU citizens in Scotland through these uncertain times."
The study, a collaboration between RGU and Feniks – a charity aiming to improve the wellbeing of the Central Eastern European Community in Edinburgh – aimed to analyse how this seismic change in British politics is shaping the lives of the communities most affected.
Piotr Teodorowski, an early career researcher at RGU involved in the study said: “Many EU citizens now feel unwelcome and rejected, with some reporting experiences of discrimination. This, coupled with feelings of being marked out as different, disenfranchised, and disempowered, express the anxiety felt by EU citizens in Scotland as a result of Brexit.
“The underlying argument we can draw from this research is that the mental health of EU citizens is important, not only in its own right, but as a barometer of integration and cohesion in Scotland. We hope these results will help to stimulate debate on how EU citizens in Scotland can be supported and how to enhance cohesion in Scottish society."