In addition to proper physicochemical properties, low toxicity is also desirable when seeking suitable ionic liquids (ILs) for specific applications. In this context, machine learning (ML) models were developed to predict the IL toxicity in leukemia rat cell line (IPC-81) based on an extended experimental dataset. Following a systematic procedure including framework construction, hyper-parameter optimization, model training, and evaluation, the feedforward neural network (FNN) and support vector machine (SVM) algorithms were adopted to predict the toxicity of ILs directly from their molecular structures. Based on the ML structures optimized by the five-fold cross validation, two ML models were established and evaluated using IL structural descriptors as inputs. It was observed that both models exhibited high predictive accuracy, with the SVM model observed to be slightly better than the FNN model. For the SVM model, the determination coefficients were 0.9289 and 0.9202 for the training and test sets, respectively. The satisfactory predictive performance and generalization ability make our models useful for the computer-aided molecular design (CAMD) of environmentally friendly ILs.