At about 8 p.m., deputies were called to the 19900 block of Streit Road for a well-being check, according to a sheriff's statement.
Upon arrival, a man walked out of the home with a firearm, police said.
Deputies fired their gun during a confrontation with the man, striking him, the statement said.
He was transported to Mercy Harvard Hospital and later flown to Javon Bea Hospital in Rockford where he remains in critical condition, police said.
McHenry County Major Investigation Assistance Team will be handling the investigation.