Switzerland was among a number of countries that halted their contributions to UNRWA earlier this year amid suspicions that the organisation had misused donor funds.
The organisation also faced allegations of "serious ethical abuses" by the management, including its then chief, Pierre Krahenbuhl, a Swiss citizen who resigned last month.
In early November, UN Secretary General Antonio Guterres released a statement saying the preliminary findings of an internal UN probe found no "fraud or misappropriation of operational funds" by Krahenbuhl.
"There are, however, managerial issues that need to be addressed," his statement said.
The Swiss foreign ministry told AFP in an email on Friday that Guterres had confirmed in a letter sent to Bern on December 3 that "the probe uncovered no evidence of misappropriation of funds".
The ministry also highlighted reforms put in place by UNRWA to better manage donor funds.
"Taking into account the measures taken and the confirmation from the UN Secretary-General that no donor funds had been misappropriated, (Switzerland) has decided to resume its payments to UNRWA," it said.
Before halting its payments to the agency, Switzerland had already dished out 25 million Swiss francs ($25.4 million, 23 million euros) in 2019.
In 2018, the wealthy Alpine nation provided the organisation with funds of 26 million francs.
Even before the accusations of misappropriation emerged, UNRWA faced a severe funding crunch, after US President Donald Trump decided last year to suspend, then yank entirely his country's contribution to the agency's budget, robbing it of its top donor.
Trump's administration, along with Israel, accuses UNRWA of perpetuating the Israeli-Palestinian conflict.
The agency disputes that and says the services it provides would otherwise not be available to Palestinians.
UNRWA was set up in the years after more than 700,000 Palestinians were expelled or fled their lands during the 1948 war surrounding the creation of Israel.
It provides schooling and medical services to millions of impoverished refugees in Jordan, Lebanon and Syria as well as the Palestinian territories, and employs around 30,000 people, mostly Palestinians.
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