The traditional way of diagnosing malaria takes time, as physicians have to check about 5000 cells to produce the final report. The accuracy of the final report also depends on the physician’s expertise. In the event of a malaria epidemic, a shortage of qualified physicians can become a problem. In the manual method, the parasites are identified by visual identification; this technique can be automated with the use of new algorithms. There are numerous publicly available image datasets containing the intricate structure of parasites, and deep learning algorithms can recognize these complicated patterns in the images. This study aims to identify and localize malaria parasites in the photograph of blood cells using the YOLOv5 model. In this research, a publicly available malaria trophozoite dataset is utilized which contains 1182 data samples. YOLOv5, with the novel technique of weight ensemble and traditional transfer learning, is trained using this dataset, and the results were compared with the other object detection models—for instance, Faster RCNN, SSD net, and the hybrid model. It was observed that YOLOv5 with the ensemble weights yields better results in terms of precision, recall, and mAP values: 0.76, 0.78, and 0.79, respectively. The mAP score closer to 1 signifies a higher confidence in localizing the parasites. This study is the first implementation of ensemble YOLOv5 in the malaria parasite detection field. The proposed ensemble model can detect the presence of malaria parasites and localize them with bounding boxes better than previously used models.