But it was not an easy passage for the Premiership side, although they were only really under pressure for a 15-minute spell in the second half.
In midfield Scunthorpe's Matt Sparrow had a very creative and industrious game, while City's Matthew Upson and Martin Taylor always held the upper hand against the lightweight Scunthorpe attack of teenagers Billy Sharp and Andy Keogh.
Both sides showed one another great respect at the outset and initially it was Scunthorpe that got a toe-hold in the game forcing two successive corners from Wayne Corden that made the Birmingham defence look uncomfortable.
Scunthorpe escaped punishment after 12 minutes, Mikael Forssell's shot taking a deflection off skipper Andy Crosby and keeper Paul Musselwhite did well to turn the ball onto a post.
That piece of fortune did not last long as the visitors took a 15th minute lead. Julian Gray crossed from the left and the ball fell kindly for Forssell to crack home his first goal of the season.
The goal settled the Premiership side down and Jermaine Pennant's fine cross was headed wide by Walter Pandiani.
However Scunthorpe did not drop their heads and Corden forced a fine save from Nico Vaesen. He then hit a smart shot over the top and the keeper then did well to get down to another free-kick, this time struck fiercely by Richie Ryan.
Birmingham came under a great deal of pressure as the second half opened and Sharp thought he'd equalised in the 62nd minute, but his strike partner Keogh was ruled offside.
Just as the Midlands side looked to be rocking a little they received a lifeline when Jamie Clapham was brought down in the box by Crosby and Forssell stepped up to crack home the 69th minute penalty.
That literally brought a premature end to the game as the visitors took control, stroking the ball around with some ease against the tired legs of what was an inexperienced home side.