In August, the centre-back suffered a relapse of a ruptured Achilles he picked up in a Scottish Cup win over Rangers at Tynecastle Park in February.
Souttar is understood to have sustained it while running as he made his way back to fitness for the new season.
Neilson revealed good news for the 24-year-old with his rehab set to move to the next level at the end of the month.
Frustratingly for the manager and Hearts, they reckon the relapse was due to the lockdown and restrictions which impacted his progress.
"John's good actually,” Neilson said. “He's still got the boot on but that comes off the end of this month and he starts building up again. We're just hoping everything will be fine this time.
"We think that having the operation then having the lockdown when he couldn't get any treatment or any real physio work on it, has hopefully been the issue.
"We're hoping this time that getting the op then getting physio every day, it will help him get back to full fitness."
Souttar’s time at Hearts has been beset with injuries.
He suffered a rupture of the Achilles tendon in January 2017 before having hip and ankle issues prior to the injury sustained against Rangers.
Despite missing large chunks of action, Souttar has still made more than 120 appearances for the club since joining from Dundee United and earned international recognition.