The loss was largely the result of a $25.2 million pretax charge related to the early debt repayment.
Quarterly revenue was $645.9 million, up 3.8% from 2011, but less than the $647 million analysts had estimated, the Wall Street Journal noted.
EPS, excluding the charge, was 5 cents, which matched Wall Street forecasts.
Shares of Wendy’s rose fractionally in Thursday afternoon trading.
The burger chain is continuing to change its menu and update the appearance of its restaurants as it attempts to reclaim lost market share. The company expects to open 20 new restaurants this year, 17 of which will use new designs meant to entice customers.
Sales at North American restaurants open at least 15 months increased 3.2% during the quarter. The operating margin at company-owned North American locations increased from 13.9% last year, to 14.1%.