Skin lesions encompass a variety of skin abnormalities, including skin diseases that affect structure and function, and skin cancer, which can be fatal and arise from abnormal cell growth. Early detection of lesions and automated prediction is crucial, yet accurately identifying responsible regions post-dominance dispersion remains a challenge in current studies. Thus, we propose a Convolutional Neural Network (CNN)-based approach employing a Customized Transfer Learning (CTL) model and Triple Attention (TA) modules in conjunction with Ensemble Learning (EL). While Ensemble Learning has become an integral component of both Machine Learning (ML) and Deep Learning (DL) methodologies, a specific technique ensuring optimal allocation of weights for each model’s prediction is currently lacking. Consequently, the primary objective of this study is to introduce a novel method for determining optimal weights to aggregate the contributions of models for achieving desired outcomes. We term this approach “Information Gain Proportioned Averaging (IGPA),” further refining it to “Multi-Level Information Gain Proportioned Averaging (ML-IGPA),” which specifically involves the utilization of IGPA at multiple levels. Empirical evaluation of the HAM1000 dataset demonstrates that our approach achieves 94.93% accuracy with ML-IGPA, surpassing state-of-the-art methods. Given previous studies’ failure to elucidate the exact focus of black-box models on specific regions, we utilize the Gradient Class Activation Map (GradCAM) to identify responsible regions and enhance explainability. Our study enhances both accuracy and interpretability, facilitating early diagnosis and preventing the consequences of neglecting skin lesion detection, thereby addressing issues related to time, accessibility, and costs.