Murray beat Djokovic to win Wimbledon in 2013 but since then has lost their last five slam meetings, including finals at the last two tournaments.
Djokovic is a heavy favourite to win his fifth slam title in a row next Sunday and appears more dominant than ever.
Rafter, who won the US Open in 1997 and 1998 and was twice a runner-up at Wimbledon, said: “This probably isn’t nice for him to hear but he’s probably in a slightly different league.
“Novak’s just a little bit better than Andy. But he’s already won two slams and made 10 finals. That’s how good he is. Unfortunately he’s up against some of the greatest of all time.
“You’ve seen all the guys go on their little runs – when Nadal was playing well, you thought there’s no way this guy’s going to get beaten. And the same with Novak right now. He will have his time and then it’ll be over. But right now he’s right in the middle of his good run.”
Murray will hope his best season on clay can translate onto grass, the surface he still regards as his most productive.
Next up for Murray is today’s clash with Chinese Taipei’s Lu Yen-hsun, who has decent Wimbledon pedigree having beaten Andy Roddick in 2010 to reach the quarter-finals and previously knocking Murray out of the 2008 Beijing Olympics.
The world No 76 also goes into the meeting on an 11-match winning streak after back-to-back Challenger titles in Surbiton and Ilkley and a first-round victory against Alexander Kudryavtsev.
Murray beat Lu at Wimbledon in 2013 and at Queen’s last year, and he said: “It’s a very tough match. He’s played the three grass-court Challengers in the build-up. He’s won two of them and lost in the final of one.
“He’s made the quarters at this event before, beat Roddick once. He plays well on the grass. It will be a really, really tough match, and a good test for me.”
Lu, 32, came back from six months out following elbow surgery in May and has surprised himself with his results.
“I didn’t expect to play so many matches at these three Challengers,” he said. “But I’ve just come back from injury and that is why I decided to start at these small tournaments.
“I hoped to play more matches to get this match feeling. In the first week I made the final and got more confidence. I was not expecting so much but I kept winning.”
Willis dream is over: Page 20