The kitten was evaluated by the Pennsylvania SPCA Veterinary staff and was determined to be suffering from a concussion and cuts and bruises.
The kitten, named "Tostino" by the PSPCA staff, has responded well to treatment and his prognosis is good. However, he will remain under close observation in the shelter hospital for at least a week.
The PSPCA said Tostino suffered a severe concussion and was bleeding from the nose and ears when he was found.
Two juvenile boys, ages 15 and 16, were arrested by officers and were charged with one count of misdemeanor animal cruelty, which is punishable by a fine of no less than $1,000 and up to two years in jail.
The Pennsylvania SPCA was called to the 4500 block of G Street in Juniata on Wednesday after a neighbor witnessed the jaw dropping deed.
Officers say two teen boys closed the cat in a microwave and threw it out the window.
"Just did it more or less as a prank. The cat was found on the street about four days ago, they kept it in the house and just decided they didn't want it, decided to throw it out of the third story window," Pennsylvania SPCA spokesman George Bengal said.
When officers arrived, the cat was still trapped in the microwave.
Friends of the teens tell Action News the boys are students at Olney High School.
"It's a shame, because they're my friends and they're in trouble right now," friend Angel Morat said.
Action News is told the teens shot video of the entire incident which is now in the hands of authorities.
A Chihuahua was also removed from the home.
Bengal says the conditions the dog was living in weren't the best, but it was otherwise in good condition.
Tostino will not be available for adoption until he is fully healed and well enough to leave the shelter.