The participants in the commemorative run wore T-shirts bearing peace slogans.
One of the organisers of the run, Ali Awdoll, told the BBC that the attack had made a lasting impression on the residents of Garissa.
"As we try to mourn the innocent lives, it's like it happened yesterday. The images of the dead bodies keep on playing in my mind. It was really a traumatising experience."
He said the runners were participating as "a gesture of the peace and humanity that we lost... there is no 'we' and 'they' in this whole thing - we are humanity and we all have one common enemy - the terrorists are our common enemy".
Garissa Township MP Aden Duale was one of those taking part.
He said: "Together as a country, from the north to the south to the west to east, from the Muslims to Christians... together we must fight all forms of terror."
Security was tight in and around the college in Garissa, 365km (225 miles) north-east of the capital.
This is in stark contrast to the time of the attack, when only two guards were on duty, despite official warnings that an attack on an institution of higher learning was likely.
The four gunmen were killed during the siege but it took 16 hours for anti-terrorism forces to bring the attack to an end.
Garissa university campus
1. Militants enter the university grounds, two guards are shot dead
2. Shooting begins within the campus
3. Students attacked in their classrooms while preparing for exams
4. Gunmen believed isolated in the female dormitories