Background Patients with inflammatory bowel disease (IBD) often have low levels of physical activity, which may be related to kinesiophobia. However, the associations of independence in basic activities of daily living, fatigue, and disease activity with kinesiophobia remain insufficiently understood. This study examined factors associated with kinesiophobia in patients with IBD, focusing on independence in basic activities of daily living and fatigue. Methods A cross-sectional study included 249 patients with IBD recruited from a tertiary hospital in Shanghai, China, between June and October 2025. Kinesiophobia was assessed using the Tampa Scale for Kinesiophobia-17 (TSK-17), independence in basic activities of daily living using the Barthel Index, and fatigue using the Multidimensional Fatigue Inventory (MFI-20). Disease activity was assessed using disease-specific clinical indices and classified into common activity categories. Multiple linear regression analyses were used to examine factors associated with kinesiophobia. An expanded covariate-adjusted model and sensitivity analyses assessed consistency of findings. Results The mean TSK-17 score was 38.84 ± 10.02, and 142 patients (57.0%) scored at or above the descriptive threshold of 37. Lower independence in basic activities of daily living (B = −0.284, β = −0.561, P < 0.001) and greater fatigue (B = 0.097, β = 0.171, P = 0.001) were associated with greater kinesiophobia. The Barthel Index had the largest absolute standardized coefficient. Female sex and medical insurance type were associated with kinesiophobia. Moderate disease activity was associated with greater kinesiophobia than lower clinical activity (remission or mild disease activity), whereas severe disease activity was not. The associations with independence in basic activities of daily living and fatigue remained significant across expanded and sensitivity analyses, whereas the association with disease activity varied across analytical approaches. Conclusion Kinesiophobia in patients with IBD was more consistently associated with lower independence in basic activities of daily living and greater fatigue than with disease activity. These findings underscore the relevance of patients' everyday functioning and symptom burden when evaluating movement-related concerns. Considering these dimensions alongside disease activity may support more comprehensive assessment of movement-related concerns and a more individualized approach to physical activity in IBD care.