The blaze at Oldtown Street was reported around eight o'clock this morning.
A spokesperson for the NI Fire and Rescue Service said the flat was well alight when Firefighters arrived.
"Using a ladder they rescued a man in his 30’s from a front window. He was taken to hospital by Ambulance.
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"The cause of the fire is believed to be deliberate and PSNI are investigating. The incident was dealt with at 8.27am."
Two appliances from Cookstown and two from Dungannon attended the incident.
Local Councillor Trevor Wilson praised the emergency services for their prompt response and rescue. "I hope the person makes a full and speedy recovery," he said.
Mid Ulster MLA Keith Buchanan also commended the emergency services.
“I commend the NIFRS who responded quickly to the incident and my thoughts are with the person who was injured and I wish him a speedy recovery,” he said.
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