Fraidenburg said CHIME's Healthcare CIO certification is highly complex, as it incorporates business-side requirements along with technical knowledge. The course is so difficult that even he didn't pass it the first time around.

But, Fraidenburg noted that workers with vendor-specific certifications, particularly in EHR deployment, are also highly sought after.

"Healthcare is definitely one of the most significant areas of growth, and it requires the most skilled people," Fraidenburg said. "It's the ultimate matrix management. Each part of the organization is fully dependent on other parts: patient care feeds into house keeping. In the payer space, care management and financial are related."

What employers are looking for

According to Fraidenburg, the most coveted IT certifications are the Project Management Professional for clinical systems and Electronic Health Records (EHR) deployment and administration, both for healthcare organizations and the vendors that sell the products.