Organised by Nike NZ's Running Co-ordinator Lydia O'Donnell, 25, the event was designed to eliminate fears in the community following the attack on Ms Pert.
"I'm an elite marathon runner so do a lot of running and running around Auckland by myself," she said.
"I organise a lot of events through work and do coaching and after what happened in Auckland last week with the attack I have had quite a lot of girls who have been in touch with me freaking out about running in Auckland and running alone.
"I thought, 'screw that, that's not fair -- we should be able to get out and get running whenever we want'. And this is a way to honour Jo and her love of running."
Ms O'Donnell said she did not know Ms Pert, but was among a large number of avid joggers deeply shocked by her death.
"I don't know Jo at all but she's a runner so she must be a good person. A lot of girls have been in contact, they were freaking out about going running in the streets.
"I don't think it is fair for this community to have barriers to be able to get out and train and run."
Run For Her will start at Victoria Park at 11am on Saturday, and follow a course through the waterfront and Westhaven.
Runners of all ability were welcome, and did not have to run the full 5km if they did not feel up to it, said Ms O'Donnell.
The event has 73 people registered as attending, with a further 292 "interested".
Ms O'Donnell said everyone was welcome -- including men.
On the event's page, many have expressed their support for the initiative and spoken about their fears of running since Ms Pert's attack.