Iranian news agency Mehrnews said the "missile and drone" attack targeted the Jaish al-Adl group's headquarters in Pakistan, calling it "another decisive step taken by Iran in response to the aggression against the security of our country".
The strike came late on Tuesday after Tehran also launched attacks in Iraq and Syria against what it called "anti-Iranian terrorist groups".
Pakistan denounced the strike, near the nations' shared border.
"Last night's unprovoked and blatant breach of Pakistan's sovereignty by Iran is a violation of international law and the purposes and principles of the Charter of the United Nations," spokeswoman Mumtaz Zahra Baloch said in a statement on Wednesday.
The foreign ministry recalled its ambassador from Tehran and said Iran's envoy -- currently on a visit home -- would not be allowed to return to Islamabad.
Tehran's top diplomat insisted his country's armed forces had targeted "Iranian terrorist group" Jaish al-Adl in Pakistan.
"None of the nationals of the friendly and brotherly country of Pakistan were targeted by Iranian missiles and drones," Foreign Minister Hossein Amir-Abdollahian said on the sidelines of the World Economic Forum in Davos, Switzerland.
Formed in 2012, Jaish al-Adl is blacklisted by Iran as a terrorist group and has carried out several attacks on Iranian soil in recent years.
The Iranian foreign ministry said Amir-Abdollahian spoke with his Pakistani counterpart Jalil Abbas Jilani on Wednesday, stressing that "Pakistan's sovereignty and territorial integrity are of great concern".
Amir-Abdollahian said "Jaish al-Adl is a terrorist group that acts against the common security of the two countries", according to a summary of the conversation released by Tehran.
Iran had earlier launched missile attacks on "spy headquarters" and "terrorist" targets in Syria, and Iraq's autonomous Kurdistan region.
- 'No limits to security' -
The Iranian strikes add to multiple crises across the Middle East, with Israel waging a war against Hamas in Gaza and pro-Palestinian Huthi rebels in Yemen attacking commercial vessels in the Red Sea.
On Wednesday, Iran's Defence minister Mohammad Reza Ashtiani said Tehran would set "no limits" to its security.
China, close partners of Iran and Pakistan, urged restraint, with foreign ministry spokeswoman Mao Ning saying both should "avoid actions that would lead to an escalation of tension".
The United States condemned the Iranian strikes in Pakistan, Iraq and Syria, with State Department spokesman Matthew Miller saying Tehran has violated the "sovereign borders of three of its neighbors in just the past couple of days".
Pakistan's official statement did not specify where the strike took place, but Pakistani media said it was near Panjgur in southwest Balochistan province, where the countries share a sparsely populated border of nearly 1,000 kilometres (620 miles).
Hours before the strike, Pakistan's caretaker Prime Minister Anwar-ul-Haq Kakar had met the Iranian foreign minister on the sidelines of the WEF.
"This violation of Pakistan's sovereignty is completely unacceptable and can have serious consequences," Pakistan's foreign ministry statement said.
It said the strike caused the "death of two innocent children while injuring three girls".
- 'Common threat' -
Jaish al-Adl claimed responsibility for an attack in December on a police station in Rask that killed at least 11 Iranian police officers.
The United States has also labelled Jaish al-Adl a terrorist organisation, saying the group "primarily targets Iranian security personnel" but also government officials and civilians with assassinations, kidnappings, and suicide bombings.
Tehran and Islamabad frequently accuse each other of allowing militants to operate from the other's territory to launch attacks, but it is rare that official forces on either side engage.
"It is even more concerning that this illegal act has taken place despite the existence of several channels of communication between Pakistan and Iran," Pakistan's foreign ministry said.
"Pakistan has always said terrorism is a common threat to all countries in the region that requires coordinated action."
Michael Kugelman, director of the South Asia Institute at the Washington-based Wilson Center, warned of the seriousness of the strike.
"Iran has staged cross-border operations against Pakistan-based militants in the past, but I don't recall anything on this scale," he said on X, formerly Twitter.
"This plunges Pakistan-Iran ties -- a delicate relationship even in the best of times -- into serious crisis."
- 'Act of aggression' -
Iraq recalled its ambassador from Iran on Tuesday after deadly missile strikes by its ally on its autonomous Kurdish region.
Four people were killed and six others wounded in the attack, according to the Kurdistan security council.
Iraq challenged Iran's claim that the strikes targeted Israel's intelligence services in response to recent Israeli assassinations of Iranian and pro-Iranian commanders.
It said it would lodge a complaint with the UN Security Council over the Iranian "attack on its sovereignty".
Iran defended its missile strikes in Iraq and Syria, saying they were a "targeted operation" and "just punishment" against those who breach the Islamic Republic's security.
Iran's Revolutionary Guards said they had destroyed the "Zionist regime's spy headquarters in the Kurdistan region of Iraq".
Iran has made support for the Palestinian cause a centrepiece of its foreign policy since the 1979 Islamic revolution.
It supports Palestinian militant group Hamas and hailed its deadly October 7 attacks on Israel as a "success" while denying any direct involvement.
Regional tensions have spiked since, drawing in Iran-backed armed groups in Lebanon, Iraq, Syria and Yemen.
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