A total of 4,358 patients were approved for treatment in other EU countries in the last five years, until the UK completed its transition period out of the EU at the end of 2020.
Some 52 patients who applied before that date are still waiting for a decision on whether they can obtain healthcare in the EU.
Last week, the Health Minister announced a scheme to fund cross-border healthcare after Brexit, but this scheme is unlikely to meet the same level of demand for NI citizens as was awarded under membership to the European Union.
The figures were revealed in a written answer to Foyle SDLP MLA Sinéad McLaughlin.
She said: “Brexit has deprived patients in Northern Ireland of the option to obtain free health treatment in EU countries.
“Given the scandalously long waiting times and waiting lists here, it should be no surprise that over 4,000 patients availed of this in recent years.
“It is a crying shame that this avenue to escape our excessively long waiting lists has now been taken away from our patients as part of Brexit.
“It is one of the many perks of EU membership that Leave campaigners overlooked during their campaign. The promised £350m a week for the NHS was never delivered by Brexit.
“Instead we have lost access to world class medical facilities in our neighbouring countries.”