The $45 million included about $25 million in lost revenue and about $20 million in additional operating costs, primarily related to passenger re-accommodation expenses.
That led cost per available seat mile, excluding special items and fuel, to rise 10% to 5.83 cents. Adjusted operating expense rose 25% to $567.5 million.
Shares were down 17% in early afternoon trading.
Spirit and its pilots, represented by the Air Line Pilots Association, are negotiating under the supervision of the National Mediation Board.
Cowen & Co. analyst Helane Becker said Thursday that she is concerned by the possibility of additional pilot job actions. "We believed there will be a continued headwind from the pilots until a deal is reached, which could force the company to be more conservative with their capacity outlook," Becker wrote in a note.
Excluding items, the carrier earned $79.1 million, or $1.14 a share, in the second quarter. Analysts had estimated $1.10. Operating margin excluding items was 19.1%. Revenue rose 20% to $701.7 million. Return on invested capital for the 12 months ended June 30 was 20.3%.
Total revenue per available seat mile gained 5.7% as capacity gained 9.3%. Without the cancellations, TRASM would have gained about 6.5% and adjusted CASM ex-fuel would have been up about 2%, Spirit said.
"The progress we made with our revenue initiatives, as well as the underlying revenue trends as we headed into the June quarter, were encouraging," said CEO Bob Fornaro in a prepared statement.
"Unfortunately, given the level of operational disruptions and the associated financial impact, the second quarter 2017 performance overall was disappointing," Fornaro said.
Chief Financial Officer Ted Christie said, ""While our cost performance for the second quarter was not satisfactory, we do not believe it materially changes our long-term cost outlook and are confident that we will continue to maintain, or grow, our relative cost advantage."