Introduction: Fertility is fundamental to human well-being, significantly impacting both individual lives and societal development. In particular, sperm morphology—referring to the shape, size, and structural integrity of sperm cells—is a key indicator in diagnosing male infertility and selecting viable sperm in assisted reproductive technologies such as in vitro fertilisation (IVF) and intracytoplasmic sperm injection (ICSI). However, traditional manual evaluation methods are highly subjective and inconsistent, creating a need for standardized, automated systems. Objectives: This study aims to develop a robust and fully automated sperm morphology classification framework capable of accurately identifying a wide range of morphological abnormalities, thereby minimizing observer variability and improving diagnostic support in reproductive healthcare. Methods: We propose a novel ensemble-based classification approach that combines convolutional neural network (CNN)-derived features using both feature-level and decision-level fusion techniques. Features extracted from multiple EfficientNetV2 variants are fused and classified using Support Vector Machines (SVM), Random Forest (RF), and Multi-Layer Perceptron with Attention (MLP-Attention). Decision-level fusion is achieved via soft voting to enhance robustness and accuracy. Results: The proposed ensemble framework was evaluated using the Hi-LabSpermMorpho dataset, which contains 18 distinct sperm morphology classes. The fusion-based model achieved an accuracy of 67.70%, significantly outperforming individual classifiers. The integration of multiple CNN architectures and ensemble techniques effectively mitigated class imbalance and enhanced the generalizability of the model. Conclusions: The presented methodology demonstrates a substantial improvement over traditional and single-model approaches in automated sperm morphology classification. By leveraging ensemble learning and multi-level fusion, the model provides a reliable and scalable solution for clinical decision-making in male fertility assessment.