Abstract: A system for predicting an activity of small Cas9 using deep learning, including a sequence input unit receiving input data on a guide sequence and target sequence of small Cas9, a predictive model generator generating a small Cas9 activity predictive model by performing deep learning for learning a relationship between small Cas9 activity data obtained from the input data on the guide sequence and target sequence of small Cas9 received from the sequence input unit and features that affect small Cas9 activity, a candidate target sequence input unit receiving candidate target sequence of small Cas9, and an activity predictor predicting small Cas9 activity by applying candidate target sequence input in the candidate target sequence input unit to the predictive model generated in the predictive model generator.