Demonstrators handed out thousands of leaflets bearing the message "only independence can defend Hong Kong and protect its people" at about a dozen campuses.
Chinese President Xi Jinping warned on a visit in July any threat to China's sovereignty "crosses the red line and is absolutely impermissible."
But activists have remained defiant, with pro-independence banners appearing at university campuses across the city in September despite a ban.
Tuesday's campaign targeting secondary school students was spearheaded by the groups "Studentlocalism" and "Hong Kong National Front", who said they were exasperated with calls for a democratic China.
"I believe when you talk about liberating the whole of China, Hong Kong independence is relatively more possible," said the convener of Hong Kong National Front, who only identified himself as Louis.
The 20-year-old added schools were "an important battle line for the independence movement".
Pro-Beijing lawmaker Felix Chung urged the authorities to step in, adding the city's mini-constitution states that the territory is part of China.
"It's ridiculous, targeting some immature, young students," said Chung of the Liberal Party.
Independence calls grew out of the failure of mass Umbrella Movement rallies in 2014 to win democratic reform for Hong Kong and have been fanned by growing concerns that Beijing is tightening its grip on the city.