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Circular RNAs (circRNAs) are covalently closed RNA molecules, and have been identified in many crops. However, there are few datasets for circRNA junctions from common wheat during <i>Fusarium</i> head blight disease. In the present study, we used RNA-seq to determine the changes in circRNAs among the control (CK) and 1, 3, and 5 days post-<i>Fusarium graminearum</i> inoculation (dpi) samples. More than one billion reads were produced from 12 libraries, and 99.99% of the reads were successfully mapped to a wheat reference genome. In total, 2091 high-confidence circRNAs—which had two or more junction reads and were supported by at least two circRNA identification algorithms—were detected. The completed expression profiling revealed a distinct expression pattern of circRNAs among the CK, 1dpi, 3dpi and 5dpi samples. This study provides a valuable resource for identifying <i>F</i>. <i>graminearum</i> infection-responsive circRNAs in wheat and for further functional characterization of circRNAs that participated in the <i>Fusarium</i> head blight disease response of wheat.