The 85-year-old leader appeared in a video aired by state media on Saturday, which showed dozens of people attending an event at a mosque to mark Ashura, the holiest day of the Shia Muslim calendar.
In the footage, Khamenei is seen waving and nodding to the chanting crowd, which rose to its feet as he entered the mosque.
State TV said the clip was filmed at the Imam Khomeini Mosque in central Tehran.
Khamenei has avoided public appearances since the start of the fighting on June 13, and his speeches have all been prerecorded.
The United States, which joined in the Israeli attacks by bombing three key nuclear sites in Iran on June 22, had sent warnings to Khamenei, with US President Donald Trump saying on social media that Washington knew where the Iranian leader was, but had no plans to kill him, “at least for now”.
On June 26, in prerecorded remarks aired on state television, Khamenei rejected Trump’s calls for Iran’s surrender, and said Tehran had delivered a “slap to America’s face” by striking a US airbase in Qatar
Trump replied, in remarks to reporters and on social media: “Look, you’re a man of great faith. A man who’s highly respected in his country. You have to tell the truth. You got beat to hell.”
Iran has acknowledged that more than 900 people were killed in the war, as well as thousands injured. Iran’s retaliatory missile attacks on Israel killed at least 28 people there.
The ceasefire between the two countries took hold on June 24.
Since then, Iran has confirmed serious damage to its nuclear facilities, and denied access to them for inspectors from the United Nations’s nuclear watchdog, the International Atomic Energy Agency (IAEA).
The IAEA’s inspectors had stayed in the Iranian capital throughout the fighting, even as Israel attacked Iranian military sites and killed several of the country’s most senior commanders and top scientists, as well as hundreds of civilians.
However, they left after Iranian President Masoud Pezeshkian signed a law suspending cooperation with the IAEA on Wednesday.
IAEA Director-General Rafael Grossi on Friday stressed “the crucial importance” of dialogue with Iran to resume monitoring and verification work of its nuclear programme as soon as possible.
Iran was holding talks with the US on its nuclear programme when Israel launched its attacks. The US has been seeking a new agreement after Trump pulled the US out of the Joint Comprehensive Plan of Action (JCPOA), which Tehran signed with world powers in 2015.
