This study examined the relationship between the study habits and reading comprehension levels of Grade 3 pupils at Dolores Central Elementary School in Eastern Samar. Motivated by the persistent learning crisis in the Philippines, particularly in early-grade literacy, the study aimed to describe pupils’ study habits, determine their reading comprehension levels, assess the significance of the relationship between the two variables, and identify which study habit dimension was most strongly associated with comprehension. Using a descriptive–correlational research design, the study involved 60 Grade 3 pupils during the School Year 2024–2025. Data were gathered through a researcher-developed Study Habits Questionnaire and a Reading Comprehension Test measuring literal, inferential, and critical comprehension. Descriptive statistics such as mean, frequency, and percentage were used to describe learners’ study habits and comprehension levels, while the Pearson Product–Moment Correlation Coefficient determined the relationship between variables. Results revealed that pupils had an overall “Good” level of study habits (M = 3.13), although reading frequency and test preparation were “Fair.” Their overall reading comprehension level was “Beginning,” with particular difficulty in inferential and critical comprehension. A moderate positive correlation (r = 0.462, p = 0.001) indicated that better study habits were associated with higher comprehension performance, with reading frequency showing the strongest association. The study concludes that strengthening reading-related study habits can significantly improve pupils’ comprehension outcomes and recommends enhancing structured reading routines both at home and in school.