The Tigers were afforded the perfect start when Tom Eaves, on his first start since early January, scored his first goal in the league since December 2 to put the leaders ahead.
The hosts spurned chances to make it two, most notably when Jacob Greaves produced a contender for miss of the season when he headed against the woodwork in the second half.
Gillingham levelled in the 67th minute when Olly Lee netted after Hull switched off and failed to clear a corner from Thomas O'Connor, although McCann felt that Alfie Jones was fouled in the build-up.
Jones - who moved into defence due to the absence of Reece Burke, who missed the game with a calf injury - received lengthy treatment and was substituted after going down in a heap following a goalmouth scramble.
He is likely to have to go through a five-day concussion protocol before being cleared to play, while Burke could be out for two to three weeks with a calf issue.
Offering his take on the game, which saw Hull extend their unbeaten sequence to seven matches but promotion rivals Sunderland and Peterborough United both make up ground on them following victories, McCann said: "I thought the performance was good and in the way we played on the ball and created opportunities and it was much more like us. We did not show that (at Shrewsbury) last week.
"It was a really good goal from Tom to give us the lead. It was good play from Mallik (Wilks) and great play from Tom and he nearly scored against to make it two-nil when he hit the post with a little snapshot against the post.
"We were up against a team who play a certain way and you have to defend your box and pick up second balls and I thought we did that for the majority of the game.
"It was just one lapse in concentration from a corner. I actually think it was a free-kick to us because their centre-half had his hands around Alfie Jones and he did not give it.
"Then we switched off from the second phase and they play for set-plays. Even before that, I thought we'd scored when Greavesy hit the crossbar and Keano (Keane Lewis-Potter) and Mallik had a couple of opportunities.
"In terms of the way we created opportunities, they gives me confidence. It is a bit of a miss from Jacob and know be disappointed and we work very hard in training on set pieces.
"I actually thought it was in and off the crossbar. It was a bit of a surprise it did not go in,
"We didn't take the chances and that was the frustrating thing. But if we keep making those chances in the next eight games, then we will be close."
On the performance of Eaves, he added: "I thought Tom was good to say he has not started a game for a few months and the goal he scored helped him settle into the game and he ran himself into the ground and it was his first start for a while.
"It was pleasing to see him score and on another day, he could have scored a couple more."