Assessing project portfolio risk (PPR) is essential for organizations to grasp the overall risk levels of project portfolios (PPs) and realize PPR mitigation. However, current research is inadequate to effectively assess PPR, which brings challenges to managing PPR. In this context, the purpose of this study is to develop a PPR assessment model via an enhanced backpropagation neural network (BPNN). First, PPR assessment criteria considering project interdependencies are determined. Second, fuzzy logic is used to obtain original data for assessment criteria. Principal component analysis (PCA) is then employed to reduce the dimensionality of assessment criteria and derive the input and output of BPNN. Third, an improved genetic algorithm (IGA) is designed to optimize the initial weights and thresholds of BPNN. On this basis, the PCA-IGA-BPNN assessment model is constructed, followed by training and testing, possessing a test accuracy of 98.6%. Finally, comparison experiments are conducted from both internal and external perspectives. For internal comparison, the proposed model yields less mean absolute percentage error (MAPE), mean square error (MSE), and root mean square error (RMSE) than PCA-GA-BPNN, IGA-BPNN, PCA-BPNN and BPNN and offers the largest convergence speed (γ). As for external comparison, the presented model produces lower MAPE, MSE, and RMSE than Decision Tree (DT), Support Vector Machine (SVM), Random Forest (RF), and K-Nearest Neighbor (KNN) and has the largest coefficient of determination (R2). Results indicate that the established model performs more satisfactorily in assessing PPR. This research enriches PPR assessment methods and provides managers with a useful tool to evaluate PPR.