Background: Patient experience and clinical quality, which are represented by preventive care measures such as cancer screening, are both widely used for the evaluation of primary care quality. The aim of this study was to examine the association between patient experience and cancer screening uptake among women in a Japanese population. Methods: We conducted a cross-sectional mail survey. The questionnaire was sent to 1000 adult female residents randomly selected from a basic resident register in Yugawara town, Kanagawa, Japan. We assessed patient experience of primary care using a Japanese version of Primary Care Assessment Tool (JPCAT) and uptake of breast and cervical cancer screening. Results: The overall response rate was 46.5%. Data were analyzed for 190 female participants aged 21–74 years who had a usual source of primary care. Multivariate logistic regression analyses revealed that the JPCAT total score was significantly associated with uptake of breast cancer screening [odds ratio (OR) per 1 standard deviation increase = 1.63; 95% CI 1.11–2.41], but not with uptake of cervical cancer screening (OR per 1 standard deviation increase = 1.47; 95% CI 0.97–2.24). Conclusions: Patient experience of primary care was associated with uptake of breast cancer screening among Japanese women. The results of our study might support the argument that patient experience of primary care and the clinical process of preventive care, such as breast cancer screening, are linked. Electronic supplementary material The online version of this article (doi:10.1186/s12930-017-0033-7) contains supplementary material, which is available to authorized users