A series of large-scale special events, including 1916 Rising commemorations, the Olympic Games and the 2016 General Election, resulted in RTÉ recording a net deficit after tax of €19.7m last year.
The broadcaster today published its annual report, which showed that it had total revenue of €337.3m - representing a rise of €3m.
Income from the licence fee was almost unchanged at €179.1m, while commercial revenue rose by €2.8m to €158.2m.
However, the cost of special events was €16m.
The company said that while there had been growth in advertising revenue and sponsorship during 2016 there had been a marked slowdown in the second half of the year.
This had been caused by Brexit uncertainty and the consequent weakening of sterling.
RTÉ’s Director General Dee Forbes said it was a "financially challenging year".
She said the costs of centenary events and coverage were "onerous" for the organisation to absorb, while commercial revenue struggled and public funding was static.
Ms Forbes added the proceeds from the recent sale of land would be used to reshape the organisation.
She said: "The current uncertainty around the TV licence fee system, both in its current performance and in how and when it might be reformed, is making it almost impossible for RTÉ and those reliant on us, to plan ahead.
She added: "The failure to reform and modernise the current TV licence system is costing jobs across the sector, causing a stark reduction on Irish-made TV programming, threatening the provision of trusted news and current affairs and is having a stifling effect on the potential of the Irish broadcasting sector as whole."
The annual report highlighted the RTÉ Reflecting the Rising events, which was attended by 750,000 people last year.
It also said the RTÉ Player had 4.2m streams, while rte.ie had an average of 54m page views each month.
Chair of the RTÉ board Moya Doherty said the board was committed to help the development of a new five-year strategy for the organisation.
She added the board had to consider the "challenges facing public service media and how we can address these".
The report also shows that Dee Forbes, whose salary is capped at €250,000, was was paid €49,652 in expenses last year.
The bulk of the expenses related to Ms Forbes relocation from the UK. The figure also includes the total tax paid where applicable.