Rev Aniko Schutz Bradwell who leads several congregations in East Lothian said society had changed since June's vote.
She claims the language used by some politicians during the campaign had made using racist language ok.
She also says she's much more nervous speaking German in public.
In quotes released by the Church of Scotland, she said: "I have been living in Scotland for 10 years, volunteering, working and studying during this time.
"Up until the referendum, I have always felt welcome here - as part of a wider society that is made up of people from different backgrounds, including their nationality.
"Now I'm much more worried about being seen as an intruder.
Rev Schutz Bradwell, who grew up behind the Berlin Wall, said she feared division was only going to grow.
She added: "I grew up in East Germany, behind a wall - with very limited opportunities to travel, learn from others, or even live abroad - I don't want us to build any more walls."
The 34-year-old has been speaking ahead of an event for EU nationals in Edinburgh this week.
First Minister Nicola Sturgeon, who visited Germany last week, will meet with those living in Scotland in an attempt to provide "reassurance and certainty" in the wake of the Brexit vote.