Flintoff was the star of England's 2-1 Ashes series win over Australia in the summer and Vaughan believes the all-rounder's workload would be "overwhelming" if he was also captain.
But Flintoff insisted he would be ready for the challenge if an opportunity to lead his country arose after Vaughan's reign.
"I think everyone in the side has got aspirations of captaining their country, if it ever came up I'd jump at the chance," Flintoff said on Thursday.
"At the moment Vaughan is doing an unbelievable job, I'm enjoying playing under him and long may it continue but if - maybe a few years down the line - there was a chance then it's obviously something you'd have to be interested in.
"He was only saying what he thinks, I've known Michael for a few years and he would have my best interests at heart so it's not something that's going to bother me or upset me."
Flintoff wants to retain the Ashes urn in a year's time and also make an impression at the World Cup the following summer.
"I want to play in a Test side ranked number one in the world, which would mean retaining the Ashes next year," Flintoff told BBC Radio Five Live.
"I want to win a World Cup, I've played in two and have not been through to the super-six stages yet. So the West Indies will be a big few months.
"I'm enjoying playing cricket with England and desperately want to play for the best side in the world."