Transport to and visiting a veterinary practice frequently is stressful for cats and their owners. Handling a fearful cat can be a challenge for the veterinary team and stress can influence physiological parameters. This study investigated whether carrier training reduced stress during a 10 min transport by car and increased compliance during the veterinary examination. A blinded randomized controlled trial with a paired sample design (training group (TG): N = 11; control group (CG): N = 11) consisting of two visits to a sham veterinary practice was carried out. After all cats had completed the first visit, the training group received 28 sessions of positive reinforcement based carrier training over a period of six weeks. Thereafter, all cats underwent the second veterinary visit. Stress levels during the car ride were assessed on video recordings using a modified version of the Cat Stress Score (CSS) (inter-rater reliability: rs = 0.81, p < 0.02) and behaviour analyses with Interact® Software (intra-rater reliability: rs > 0.90, p < 0.01). To evaluate physiological reactions, ear temperature readings were taken before and after transport. The change in parameters between visit 1 and 2 (calculated by subtracting result of visit 1 from visit 2) was used to test for differences between groups. Trained cats showed a significant reduction in CSS during the car ride (mean ± SD: TG: – 0.60 ± 0.37, CG – 0.23 ± 0.25; p = 0.007), an increase in searching for food rewards (TG: 33 ± 24 s; CG: 6 ± 7 s; p = 0.001), lip licking (median (range): TG: 18 (7–65), CG: 0 (−3 to 24); p < 0.001), changes in body posture (TG: 13 (−2 to 46), CG: 1 (−5 to 13); p = 0.01) and sitting (TG: 233 ± 146s, CG: – 4 ± 35 s; p < 0.001). The veterinary examination was significantly shorter in trained cats (TG: − 42 ± 31 (−101 to −2) s, CG: −12 ± 24 (−50 to 31) s; p = 0.010). Significant differences in the response patterns of ear temperature further indicated lower stress in the TG (e.g. Δ ear_temp: GLMM: main effect group: p = 0.022; group*experiment: p = 0.019). Training proved to be effective in reducing stress during the car ride and led to a shorter veterinary examination. Owners should be encouraged and instructed to carrier train their cats to reduce stress around veterinary visits.