"You have now formed a branch of the Resistance Front," said Khamenei, referring to Tehran-aligned armed groups across the Middle East arrayed against arch-foe Israel which is also known as the Axis of Resistance.
"As the page of history is turning, you are standing on the right side of it," he said in a letter published on his official website on Thursday.
Universities in the United States were rocked by pro-Palestinian demonstrations in April, triggering campus clashes with police and the arrest of dozens of people.
The demonstrations began at Columbia University in New York and later spread across the country as well as to Europe and elsewhere.
Tehran has reiterated support for the Palestinian militant group Hamas since the outbreak of the war in the Gaza Strip, which was triggered by the group's attack on southern Israel on October 7.
The assault resulted in the deaths of 1,189 people, mostly civilians, according to an AFP tally based on Israeli official figures.
Militants also took 252 hostages, 121 of whom remain in Gaza, including 37 the army says are dead.
Israel's retaliatory offensive has killed at least 36,171 people in Gaza, mostly civilians, according to the Hamas-run territory's health ministry
Regional tensions have since soared, drawing in Iran-backed militant groups in Syria, Lebanon, Iraq and Yemen.
Tit-for-tat escalations led to Tehran launching hundreds of missiles and rockets directly at Israel last month.
