Jenna-Louise Coleman played space-faring Oswin Oswald and a Victorian Clara before debuting as the contemporary version of the character who now travels with Matt Smith's Doctor.
"The original companion was going to be very much the Victorian governess we saw at Christmas," Gaiman - who wrote Saturday's Who episode 'Nightmare in Silver' - told the Radio Times.
"I wrote about the first ten pages and then they said they'd changed the companion from what I was expecting to something else."
Gaiman explained that he subsequently had to "reshape" his Cybermen tale to reflect the change.
"We decided they can do more weird stuff if it's now the contemporary third incarnation," he said.
Doctor Who's current series concludes this Saturday (May 18) at 7pm on BBC One.
Finale episode 'The Name of the Doctor' - written by showrunner Steven Moffat - promises to resolve the mystery surrounding Clara's multiple identities.
> Doctor Who: Series 7 finale 'The Name of the Doctor' - in pictures
Watch Digital Spy's Alex Fletcher and Morgan Jeffery talk 'Nightmare in Silver' in the most recent Geek TV: