The demonstrators waved placards and chanted slogans as they marched on the streets of the Kenyan capital and the northeastern town of Garissa, where the massacre was carried out.
"We are mourning the loss of our fellow comrades, we have lost the vibrant blood that would have built tomorrow's Kenya," said Maureen Mucheri, 21, an engineering student at Nairobi University.
Later, hundreds gathered in a far quieter and deeply emotional demonstration in the capital, carrying flowers and lighting candles in front of scattered white crosses to remember those lost, at the end of the third and final day of national mourning.
Security forces meanwhile continued their hunt for those behind the university killings.
More From This Section
Earlier, in Garissa, several hundred people gathered at a rally where both Muslim and Christian leaders called for unity, with local Muslim leader Abdullahi Salat condemning the "violent and evil attack".
In Nairobi, some 200 students slapped vehicles with their hands as they marched through the streets, chanting "you are not safe, you are not safe!"
Kenyan fighter jets pounded camps belonging to the Al-Qaeda-linked insurgents in southern Somalia on Monday, but anger has been growing over allegations that critical intelligence warnings were missed.
The extremists lined up non-Muslim students for execution in what President Uhuru Kenyatta described as a "barbaric medieval slaughter".
Students in the demonstration carried placards with the slogan "147 is not just a number", referring to the death toll in the massacre - although that has since risen to 148.
The massacre, Kenya's deadliest attack since the 1998 bombing of the US embassy in Nairobi, claimed the lives of 142 students, three police officers and three soldiers.