Pulpitis, periapical disease, and deep caries (PPD) are the most common bacterial oral diseases with strong connections from the perspective of etiology. However, the underlying molecular mechanisms of PPD are not fully elucidated. Alterations of cytokines, microRNAs, long non-coding RNAs (lncRNAs), and circRNAs have been sporadically reported to be involved in the development and progress of PPD. Therefore, it is necessary to identify the candidate markers for PPD systematically. With the development of new technologies like single-cell RNA-seq and spatial transcriptomic, available datasets of PPD patients are accumulating. Therefore, we have developed Exp_PPD as a user-friendly online tool for dentists and researchers to identify potential new RNA biomarkers for PPD with cross-dataset comparison. Exp_PPD manually curated transcriptomic profiles of five different datasets of PPD with phenotype information. An intuitive querying interface was implemented to enable quick and easy searching. As the first web-based analysis tool focused on PPD, it provides detailed expression analysis of input markers in pulpitis compared to normal or in patients of different clinical statuses. Exp_PPD also facilitates the researcher in exploring the interaction network of input markers and includes a differential analysis tool to determine the expression significance of genes in two groups, particularly for in-house datasets. Exp_PPD is developed as a hypothesis generation tool for dentists and researchers to identify potential RNA biomarkers for further research aiming to accelerate the translational research of PPD.