Experienced peer support groups (EPSG) are expected to improve self-care and complement professional health care for haemophilic patients, even those living in inconvenient clinical setting. However, these benefits have not been verified quantitatively. The structural equation modelling (SEM) was used to evaluate the effects of contact with EPSG on self-care for haemophilic patients in the Japanese clinical settings. Factors affecting self-care were compared between groups with and without EPSG contact. Self-reported questionnaires were mailed to 652 haemophilic patients with HIV in Japan (September 2005–January 2006). SEM demonstrated significant associations between EPSG contact, self-care scores and other social and individual factors. The total effect of EPSG contact on self-care was calculated. The structural differences between models were analysed in a multi-group analysis. Of the 257 respondents (response rate, 39.4%), 109 reported having contact with an EPSG (EPSG+ group) and 139 reported no contact (EPSG− group). EPSG contact was significantly associated with better self-care. In the multi-group analysis, the total effect of inconvenient access to medical services on self-care in the EPSG+ group was 10% of that in the EPSG− group and was significantly associated with poor illness-related knowledge and high anxiety level only in the EPSG− group. In the EPSG+ group, patient age was strongly associated with self-care than in the EPSG− group. These findings suggest that EPSG contact may alleviate inconvenience in medical services. Factors associated with self-care differed between groups. Health care professionals must carefully assess self-care behaviours and service accessibility based on these results.