Objectives: The aim of this study was to obtain information regarding the use of flea treatments and owner-reported flea infestation and skin disease. Methods: Owners of 1150 cats were recruited into a long-term longitudinal study (‘Bristol Cats’ study) and asked to complete questionnaires at set time points. Questionnaires 1 and 5 were used and included data collection for kittens aged 2–4 months (T1) and at 2.5 years of age (T2). Owners were asked which brand of flea treatment, if any, was used at each time point. At T2 owners were asked if they had noted signs of skin disease or fleas on their cat within the previous 12 months and if they had sought veterinary attention for the skin disease or fleas. IBM SPSS version 23 was used for statistical analyses. Results: Skin disease at T2 was reported by owners of 55/1150 (4.8%; 95% confidence interval [CI] 3.7–6.2) cats. Many owners who reported skin disease (25/55 [45.5%]; 95% CI 32.3–58.7) had not sought veterinary attention. There were 81/1150 (7.0%; 95% CI 5.6–8.5) cats with reported head shaking and/or ear scratching within the past 12 months at T2. The majority of cats (204/286; 71.3%) received prescription flea treatments at both points. Use of non-prescription flea treatment at T2 was more likely to be associated with owner-reported skin disease/flea infestation than those who used prescription flea treatment (P <0.001). There was a significant association between the reported presence of fleas and reported presence of skin disease at T2 (P = 0.03). Conclusions and relevance: Despite the potential for reverse causality, the association between owner-reported skin disease and/or flea infestation in their cats and the use of non-prescription flea treatment was as expected. Use of flea treatments and, in particular, the type of ectoparasite control used (prescription or non-prescription) should be carefully assessed when managing cats with skin disease.