Israel declared UN chief Antonio Guterres "persona non grata", accusing him of failing to specifically condemn Iran's missile attack on Israel.
"Anyone who cannot unequivocally condemn Iran's heinous attack on Israel does not deserve to step foot on Israeli soil," said Foreign Minister Israel Katz in a statement.
Iran fired on Tuesday amid an escalation in fighting between its proxy in Lebanon, Hezbollah, and Israel. Many were intercepted mid-air but some penetrated missile defences. No casualties were reported.
"This is an anti-Israel Secretary-General who lends support to terrorists, rapists, and murderers," Katz said.
Katz added that Guterres, who he said supported the "murderers of Hamas, Hezbollah, the Huthis, and now Iran, the mothership of global terror, will be remembered as a stain on the history of the UN for generations to come".
Following Iran's missile attack, Guterres condemned the "broadening conflict in the Middle East", slamming "escalation after escalation" in the region.
"This must stop. We absolutely need a ceasefire," said Guterres.
Israel has been a harsh critic of the UN, with ties between the state and the international body souring even more after the .
Guterres has repeatedly called for a ceasefire to halt the fighting in both Gaza and Lebanon.