The St. Louis-based company said profit should be "at or modestly below" its target of 47 cents to 50 cents a share.
Analysts on average expected profit of 48 cents a share, according to Reuters Estimates.
The company said revenue rose 24% to $240 million, short of the average forecast for $242.8 million. Sales have benefited in recent months from Crispani, a flatbread pizza that has boosted customer traffic during evening hours.
Panera said "extreme weather" in its core markets hurt results.
It also said sales at stores open at least 18 months were unchanged from a year earlier in the quarter that ended March 27, including a drop of 0.6% at company-owned stores and increase of 0.2% in franchised stores. Total same-store sales fell 0.2% in the four weeks ended March 27.
Panera plans to report quarterly earnings on April 24. The company said it opened 31 stores in the first quarter, and operates more than 1,000 stores under the Panera Bread and Saint Louis Bread Co. brands.
Panera stock closed Tuesday at $60.22 on the Nasdaq. The shares closed one year ago at $74.96.