Security was tight but only around 20 students resumed classes at Garissa University, which had some 800 students before the massacre.
The high-profile assault on April 2, 2015 was the deadliest yet in Kenya by the Somali-led, al Qaeda-linked Shebab group. Nearly all the victims were students.
Somali militants kill 147 in Kenya university massacre
Emotions were mixed for those returning.
"I am very happy for the reopening...we went for our first lesson and we are really back to the university as normal," said Shamza Abdi, a student.
"There are some memories of a lot of our friends we lost here, but despite what happened, life must go on... we just pray for our friends," she added.
The gunmen had lined up non-Muslim students for execution in what President Uhuru Kenyatta described at the time as a "barbaric medieval slaughter".
The massacre was Kenya's deadliest attack since the 1998 bombing of the US embassy in Nairobi.
Most students, especially those who were not originally from Garissa, have transferred to other colleges. The students now returning are mainly those who come from the town, some 365 kilometres (225 miles) north of the capital Nairobi.
"We are really missing those students who were killed, and we are very bitter about it...the people of this area were really affected," said Hassan Kune Mire.
"It is very important for us that learning has resumed, and that we shall continue with our education."
University principal Ahmed Osman Warfa, speaking last week when teachers returned, said security had been tightened with a new police post built within the compound and a perimeter fence planned.
"I wish I was armed and trained on the use of firearms on that night, I would have fought with the attackers and at least ensure I have saved some of my students from their killers," the principal said.
Witnesses last week gave evidence in the ongoing trial of five men accused of supporting the attack.
Survivor from Kenya massacre emerges after two days in wardrobe
The four gunmen who carried out the massacre were all killed when Kenyan commandos stormed the building.
Survivors described how the laughing gunmen taunted their victims amid scenes of total carnage.
Students, some who had to play dead among the pools of blood of their friends until they were rescued, said the gunmen shouted "We have come to kill and be killed" as they prowled the student dormitories shooting those they found.
The Garissa attack followed the 2013 seige of the upmarket Westgate shopping mall in Nairobi, when four Shebab gunmen killed at least 67 people.
Somali rebels kill 39 in Nairobi shopping mall bloodbath
Last month Kenyan police warned of the risk of fresh attacks by Shebab insurgents, claiming they had split into rival factions inside Kenya, with some shifting allegiance from Al-Qaeda to Islamic State.
The militants say their attacks are retaliation for the Kenyan military presence in Somalia and "war crimes" committed by Kenyan troops.
Inside Somalia, they fighting to overthrow the internationally-backed government in Mogadishu, which is protected by 22,000 African Union troops, including Kenyan soldiers.
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