An automatic alarm alerted authorities to a blaze at Play to Learn Early Learning Centre's facility at Castle Hill, in Sydney's northwest, early on Monday morning.
It followed a fire at Play to Learn's Turramurra centre on Friday, which the childcare operators labelled a suspected arson attack.
Minimal damage was recorded in both fires, with an automatic sprinkler system protecting the Castle Hill facility before firefighters arrived at 1.30am on Monday.
Play to Learn said it did not know why the attacks had happened, adding there were "no grievances, disputes, or concerns internally".
"We are a tight-knit team of educators and families, and we have no reason to believe someone within our community would carry out such an act," the company's statement read.
"There are no issues involving any employees, and no internal investigations are currently underway."
Detective Superintendent Naomi Moore said the arson squad would take over the investigation.
Police believe multiple offenders forced entry at the rear of the Castle Hill premises before lighting the blaze.
"It's very concerning, there's no doubt about that.
"It's a residential street and it troubles us a lot," Det Supt Moore said.
"That's part of why the arson squad will take carriage of this, because there are two locations that could have some potential links."
Both incidents have been captured on CCTV and will be provided to police for their investigation, the childcare firm said.
Fire and Rescue NSW acting Superintendent Mathew Sigmund said the sprinkler system was activated when authorities arrived.
"(We) gained entry to the building and located what had previously been a fire, which had been extinguished by the installed fire sprinkler system," he said.
Firefighters ventilated the building before handing the scene to police.
There were no injuries in either fire.
Friday's fire damaged the foyer and the outside of the Turramurra building, along with smoke damage throughout.
Play to Learn founder and director Jade Luci said the fires were senseless and had left the community heartbroken.
"I want to reassure every family that there are no internal concerns, no staff issues, and no grievances at Play to Learn," she said.
"Our team is strong, united, and deeply committed to the wellbeing of our children."
Play to Learn has operated for 19 years and runs three centres across NSW.
Its Turramurra location opened less than two months ago.
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