Early and accurate detection of scalp hair loss is imperative to provide timely and effective treatment plans to halt further progression and save medical costs. Many techniques have been developed leveraging deep learning to automate the hair loss detection process. However, the accuracy and robustness of assessing hair loss severity still remain a challenge and barrier for transitioning such a technique into practice. The presented work proposes an efficient and accurate algorithm to classify hair follicles and estimate hair loss severity, which was implemented and validated using a multitask deep learning method via a Mask R-CNN framework. A microscopic image of the scalp was resized, augmented, then processed through pre-trained ResNet models for feature extraction. The key features considered in this study concerning hair loss severity include the number of hair follicles, the thickness of the hair, and the number of hairs in each hair follicle. Based on these key features, labeling of hair follicles (healthy, normal, and severe) were performed on the images collected from 10 men in varying stages of hair loss. More specifically, Mask R-CNN was applied for instance segmentation of the hair follicle region and to classify the hair follicle state into three categories, following the labeling convention (healthy, normal and severe). Based on the state of each hair follicle captured from a single image, an estimation of hair loss severity was determined for that particular region of the scalp, namely local hair loss severity index (P), and by combining P of multiple images taken and processed from different parts of the scalp, we constructed the hair loss severity estimation (Pavg) and visualized in a heatmap to illustrate the overall hair loss type and condition. The proposed hair follicle classification and hair loss severity estimation using Mask R-CNN demonstrated a more efficient and accurate algorithm compared to other methods previously used, enhancing the classification accuracy by 4 to 15%. This performance supports its potential for use in clinical settings to enhance the accuracy and efficiency of current hair loss diagnosis and prognosis techniques.