The Shakers lost 2-1 to Plymouth Argyle on Saturday afternoon in what was Flitcroft's first away match in charge.
"It's not going to be a quick fix. It's going to get a lot worse before it gets better," he told BBC Sport. "Two years of doing the wrong things are not going to be fixed in two games.
"I've got two years to turn it around and I'm looking forward to doing that, but it's definitely going to take time.
"I know where we're going to be at the end of the season - we'll be in League Two. There are a lot of hard games coming up but we're certainly prepared for a fight."
Bury are 23rd in the table.