Flintoff is due to play for England in the second Test against South Africa at Headingley on Friday after finally recovering from a series of ankle problems and a side strain.
Lee knows it has been a long and painful journey through rehabilitation for Flintoff and was quick to express his admiration for a rival who became a close friend during the 2005 Ashes series.
"Flintoff is a once-in-a-generation player," Lee said. "I liken him to the great Ian Botham. They are guys who can change a game at the drop of a hat with bat and ball and also field.
"He was the standout in the '05 Ashes over there, he's also a very close friend of mine but a magnificent player on and off the field.
"He's a great guy and the type of guy who can change the game. I am looking forward to having him back definitely."
Lee, 31, has been keeping a close eye on the series between England and South Africa as he prepares for a forthcoming series against the Springboks and next year's Ashes clash in England.
"I'd be lying if I say I haven't been doing a bit of homework on the series that is happening now because we have got South Africa and England coming up shortly," he said.
"I have been doing a bit of homework and watching their players. They have got a lot of young guys coming through who have been very impressive so I am looking forward to playing against both of those sides."
After helping Australia to a 2-0 Test series win over West Indies, Lee has taken some time off with his family but the Ashes are never far from his thoughts.
"I have actually tried to get away from cricket for a short period of time," he said.
"It's really good to refresh the batteries and get ready to go for what is going to be a massive summer and even a big 18 months.
"We've got the Ashes coming up as well which we are not directly looking forward to right now because we have a few things in place that we have to take care of first.
"I would be lying if I didn't say I was looking forward to the Ashes next year."