The 80-year-old Arizona Republican joked that maybe he shouldn't have stayed up late watching the Arizona Diamondbacks playing a night game out West.
"What I was trying to get at was whether Mr. Comey believes that any of his interactions with the president rise to the level of obstruction of justice," McCain said in a statement after his questioning.
Instead, McCain flummoxed Comey with a question about why "the investigation of anything former Secretary Clinton had to do with the campaign is over and we don't have to worry about it anymore?"
Comey pointed out they were separate investigations, begun at different times.
"I'm a little confused," Comey responded. "With respect to Secretary Clinton, we investigated a criminal investigation in connection with her use of a personal email server."
WATCH: James Comey addresses Senate committee at start of hearing
McCain said he doesn't understand how Comey could be done with the Clinton probe having concluded no charges were warranted, but wouldn't say the same about the Russian investigation. Comey said the Russian investigation is ongoing as far as he knows.
McCain, who can alternate between gruff and self-deprecating, afterward made light of the mess.
"I get the sense from Twitter that my line of questioning today went over people's heads," McCain said in a statement. Turning more serious, McCain said, "while I missed an opportunity in today's hearing, I still believe this question is important, and I intend to submit it in writing to Mr. Comey for the record."
The Diamondbacks joined in, retweeting McCain's statement with the "shrug" emoticon.