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We present the result of the first deep learning-based search for the signature of microlensing in gravitational waves. This search seeks the signature induced by lenses with masses between $10^3M_\odot$--$10^5M_\odot$ from spectrograms of the binary black hole events in the first and second gravitational-wave transient catalogs. We use a deep learning model trained with spectrograms of simulated noisy gravitational-wave signals to classify the events into two classes, lensed or unlensed. We introduce ensemble learning and a majority voting-based consistency test for the predictions of ensemble learners. The classification scheme of this search primarily classifies one event, GW190707_093326, into the lensed class. To verify the primary classification of this event, we also examine the median probability to the lensed class and observe the resulting value, $0.984^{+0.012}_{-0.342}$, agrees with an empirical criterion $>\!0.6$ for claiming the detection of a lensed signal. However, the uncertainty of the estimated $p$-value for the median probability and error, ranging from 0 to 0.1, convinces us GW190707_093326 is less likely a lensed event because it includes $p\!\geq\!0.05$ where the unlensed hypothesis is true. Therefore, we conclude our search finds no significant evidence of microlensing signature from the evaluated binary black hole events.