If you consider a "visit" every time someone crosses the city limits, this would be nearly impossible to calculate. If you mean tourist visits, it's an easier question to answer.
Surprisingly, despite a wealth of tourism data by country, it's difficult to find these statistics broken down by individual cities, especially for smaller nations. However, with a little detective work, I think I've figured it out.
The least visited European capitals
There are only nine European capitals with an average of fewer than 5,000 daily tourists:
1.) Vaduz, Liechtenstein 274
2.) Minsk, Belarus 319
3.) Podgorica, Montenegro 411
4.) Chișinău, Moldova 477
5.) Skopje, North Macedonia 803
6.) Monte-Carlo, Monaco 998
7.) Sarajevo, Bosnia and Herzegovina 1,790
8.) Luxembourg, Luxembourg 2,852
9.) Belgrade, Serbia 3,409
Additionally, Ljubljana, Slovenia, has approximately 3,100 tourists staying in hotels each year, but there are no figures for day visitors to the city without an overnight stay. However, there would certainly be enough day visitors to exceed 5,000.