Pardon affair and resignation
In April 2023, prior to and in commemoration of Pope Francis's pastoral visit to Hungary, Novák issued a series of presidential pardons, including that of far-right activist and domestic terrorist György Budaházy and Endre Kónya. Kónya had been the deputy director of an orphanage in Bicske who had been convicted of covering up the director's molesting of children at the institution. When Kónya's pardon—later thought to have been issued under pressure from Zoltán Balog, Novák's erstwhile mentor and synodal president of the Hungarian Reformed Church—was made public on 2 February 2024, national controversy ensued, becoming known as the "pardon affair" (Hungarian: kegyelmi ügy). Protests erupted in Budapest demanding Novák's resignation, with commentators viewing the scandal as especially damaging to Fidesz's credibility as a defender of traditional family values.
On 9 February, Novák cut short her attendance at the World Water Polo Championships in Qatar and flew home to Budapest, where she announced her resignation shortly after arriving on 10 February. In her resignation address, she also apologized to Kónya's victims. Judit Varga, who was serving as Minister of Justice in 2023 and had countersigned the pardon, also resigned as a member of parliament and withdrew her candidacy for member of the European Parliament in the 2024 election. In response, Orbán said that he would introduce a constitutional amendment to bar convicted child abusers from receiving clemency. As part of continued fallout from the scandal, Balog resigned from the synodal presidency of the Hungarian Reformed Church on 16 February 2024.
The National Assembly formally accepted, and thus made Novák's resignation effective, on 26 February 2024. She was succeeded in an acting capacity by speaker of the National Assembly László Kövér. She was the second head of state to resign in Hungary's post-communist history after Pál Schmitt, who did so in the wake of a plagiarism scandal in 2012.