Jefferies on Thursday lowered its rating of Chipotle to hold from buy, saying "valuation is full" after the stock's 65% run-up this year.

"Although we believe that there are strong fundamental drivers still to unfold for CMG ... earlier than expected loyalty program roll-out and good [same store sales] checks have propelled the stock," Jefferies analyst Andy Barish wrote in a note to investors.

"Although the company reached an impressive 1 million rewards members in barely 10 days, we think this key driver, along with the company's powerful digital drivers are now being better understood and discounted in the stock," Barish added.

Chipotle's stock was down 1.5% Thursday from Wednesday's close of $718.85 a share. Jefferies has a $700 price target on Chipotle, up from $600 previously.