The hospital became aware of the problem earlier in the week and notified authorities.
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Officials say it's unknown if there's been a breach of patient, employee or financial data.
While the hospitals are admitting and treating patients, there are some disruptions.
Elective surgeries are being prioritized by urgency, and outpatient radiology is not available, along with some cardiology testing.
Capital Health released a statement Wednesday saying:
"We continue to care for patients in both hospitals, including our Emergency Rooms, in our practices, and at all other locations under established protocols for system downtimes where necessary. We are prioritizing safe patient care while working to restore the network and address the impact of this disruption."
Rob D'Ovidio researches and teaches about cybercrime at Drexel University.
"This is purely a financial play here by the criminals. And what we've seen over the past few years with these types of attacks - there's an organized crime group behind it," said D'Ovidio.
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He says that based on other recent cyber attacks on healthcare systems, this is likely a ransomware attack - where criminals disable a server or network, demanding payment.
In August, Prospect Medical Holdings was targeted, with four hospitals in Delaware County.
D'Ovidio says the criminals are often overseas, and he's not surprised to see hospitals being compromised now.
"Pretty interesting time of the calendar year where our emergency rooms and doctors offices are filled with flu and other respiratory illnesses that come up," said D'Ovidio.
A hospital spokesperson says primary care doctors' offices are unaffected.
How long that'll last is unknown, but the hospital says they expect to operate with system limitations for at least a week.