In Chapter Eleven of Philosopher's Stone we have the following passage:
"I'm tellin' yeh, yer wrong!" said Hagrid hotly. "I don' know why Harry's broom acted like that, but Snape wouldn' try an' kill a student! Now, listen to me, all three of yeh – yer meddlin' in things that don' concern yeh. It's dangerous. You forget that dog, an' you forget what it's guardin', that's between Professor Dumbledore an' Nicolas Flamel –"
Thus – at least as far as Hagrid knew – the Stone was at that point already guarded by Fluffy. Harry didn't discover the Mirror of Erised until the next chapter, which would mean that the Stone was not protected by the Mirror at that point.
However, there is also an implication that the Stone might have already been in the Mirror at that point. In Chapter Twelve, Dumbledore explained to Harry how the Mirror works, and then explicitly mentioned that this would prepare Harry if he ever came across it again:
"The Mirror will be moved to a new home tomorrow, Harry, and I ask you not to go looking for it again. If you ever do run across it, you will now be prepared.
In Chapter Seventeen Harry thinks that Dumbledore did this purposely in order to give Harry a chance:
"No, it isn't," said Harry thoughtfully. "He's a funny man, Dumbledore. I think he sort of wanted to give me a chance. I think he knows more or less everything that goes on here, you know. I reckon he had a pretty good idea we were going to try, and instead of stopping us, he just taught us enough to help. I don't think it was an accident he let me find out how the mirror worked. It's almost like he thought I had the right to face Voldemort if I could...."
In order for this to make sense the Stone would have had to already been in the Mirror back when Harry discovered the Mirror, or at the very least Dumbledore would have had to already have thought to store the Stone there. And if he had already thought of the idea, there doesn't seem to be much reason why he wouldn't have executed it immediately. Of course, though, there wouldn't be much point in having Fluffy and all the subsequent traps if the Stone wasn't even hidden there, unless the whole third-floor-corridor thing was just a decoy.