A Matt Derbyshire penalty in the second period of extra time was enough for Rotherham United to eventually see off Fleetwood.
The Millers had the majority of the play at the New York Stadium in the first round of the Capital One cup but it was the visitors who had the first shot of the game as Paul Green was caught out and Gareth Evans shot wide.
For the most part the Millers dominated the first half and could have been well in front by the interval.
Chelsea loan teenager John Swift showed touches of class virtually every time he was in possession and was behind much of the Rotherham threat.
He had three shots, two deflected, one wide, while Jordan Bowery, Ryan Hall, Michael Tidser and Craig Morgan also had chances.
However, the Cod Army should have taken the lead just before half time as Evans found Jamie Proctor who failed to hit the target.
The second half continued just like the first, with Rotherham on top and creating nearly all the openings.
Sub Alex Revell missed a great chance to seal things in the 86th minute when he screwed his effort just wife and then Paul Green hit the post seconds later.
So the game moved into extra time, which is something the Millers could have done without, with Wolves in town this Saturday.
The first period of extra time ended goalless too but Derbyshire was upended in the box by Stephen Jordan and scored the resulting penalty kick to give Millers a one goal lead.
Rotherham United made six changes to the side which was so unlucky to lose at Derby County on Saturday for tonight’s Capital One Cup first-round tie against Fleetwood Town.
Scott Loach came in in goal and there were starts for centre-half Richard Wood, midfielders John Swift, Michael Tidser and Ryan Hall and striker Jordan Bowery.
The Championship Millers were looking for cup revenge over League One Fleetwood.
The Cod Army knocked Rotherham out of the Johnstone’s Paint Trophy 2-1 at Highbury Stadium at the Northern semi-final stage last December.
Former Millers centre-half and local boy Ryan Cresswell was among the Fleetwood subs.
Rotherham United: Loach, Broadfoot, Wood, Morgan, Skarz, Swift, Green, Tidser, Hall, Bowery, Agard. Subs: Collin, Brindley, Revell, Newton, Pringle, Sadler, Derbyshire.
Fleetwood Town: Maxwell, McLaughlin, Murdoch, Pond, Evans, Morris, Hogan, Blair, Sarcevic, Proctor, Jordan. Subs: Davies, Schumacher, Cresswell, Hughes, Ball, Campbell, Crainey.
Referee: Nigel Miller (Co Durham).