This study aims to develop a science e-module that integrates drag-and-drop interactions with the Problem-Based Learning (PBL) model to improve scientific literacy and problem-solving skills among seventh-grade junior high school students studying ecosystem topics. The low science literacy achievement of Indonesian students in PISA surveys and the predominantly procedural nature of their problem-solving abilities serve as the primary background of this research. Development was carried out using the Research and Development (R&D) method with the 4D approach—Define, Design, Develop, and Disseminate—and the product's effectiveness was tested using a One-Group Pretest-Posttest Design involving 32 seventh-grade students at MTsN 2 Karanganyar. Instruments used included subject-matter and media expert validation sheets, science literacy and problem-solving skills tests, and a student response questionnaire; content validity was established using Aiken's V (0.85–0.90), and reliability using Cronbach's Alpha (0.81–0.88). Validation results showed that the e-module received feasibility scores of 87.4% from subject matter experts and 89.1% from media experts, placing it in the "very feasible" category. Paired-sample t-tests yielded t(31) = 12.47, p < 0.001 for scientific literacy (N-Gain = 0.67, medium category) and t(31) = 14.83, p < 0.001 for problem-solving skills (N-Gain = 0.72, high category), with large effect sizes (Cohen's d = 2.20 and 2.62, respectively). Student responses to the e-module reached 91.3%, indicating a very positive reception. Thus, the drag-and-drop science e-module with the PBL model has been proven content-valid, reliable, and effective in improving scientific literacy and problem-solving skills among junior high school students.