Authorities say the suspect, 32-year-old Eduardo Sencion of Carson City, also shoot himself in the head. He later died at a hospital.
The shooting was reported at about 9 a.m. at the restaurant in a strip mall on Carson City's main street.
Witnesses said the man pulled up outside the IHOP in a blue minivan and shot a man on a motorcycle with a rifle, then walked inside the restaurant and started shooting. The gun was found to be an AK-47 assault rifle.
The names of the victims, including the three Guard members who were killed, were not immediately released. One of the Guard members killed was a man; the other was a woman, authorities said. A female civilian was also killed.
The gunman's motive was unclear, but authorities are investigating whether the military members were targeted.
The IHOP is about four miles from the Guard's headquarters complex.
"We are actively pursuing an investigation on the motive that has not been established yet," said Carson City Sheriff Kenny Furlong at a news conference Tuesday afternoon. "There has been some suggestion by his family members that there is some mental health issues that we are going to have to look into."
Extra security measures were put in place at state and military buildings in northern Nevada, but the shooting appeared to be an isolated incident, said Furlong.
The FBI and state police were on scene investigating.
"The loss of any Guardsman, whether it be a soldier or an airman or any person in the military, is a loss, and we feel it the same no matter what circumstances under which they died," said Major April Conway, Nevada National Guard.
"We are here and we grieve with the victims and their families and their friends and for all those who are touched by this tragedy," said IHOP President Jean Birch.
The FBI said it had ruled out terrorism.
The FBI planned to search Sencio's house Tuesday night.
Sencion's family said they saw Sencion Monday night, but nothing seemed wrong.
Sencion was born in Mexico and has a U.S. passport.
The Associated Press contributed to this report.