The aim of this study was to analyze the relationship between competitive anxiety and heart rate variability (HRV) in swimming athletes. A total of 66 volunteers (41 male and 27 female) who swam the 400-m freestyle in the Brazilian Swimming Championships participated. Thirty minutes before the 400-m freestyle event, the athletes answered the Competitive Anxiety Inventory (CSAI-2R) questionnaire, then underwent anthropometric (body weight, height, and skinfold thickness) and HRV measurements. Then, at a second meeting, held 3 h after the 400-m freestyle event, the athletes returned to the evaluation room for HRV measurement (Polar((R)) RS800cx, Kempele, Finland). Multiple linear regression was used to evaluate the relationship between competitive anxiety and HRV. The multiple linear regression was performed in three blocks (block 1: cognitive anxiety, block 2: somatic anxiety, and block 3: self-confidence), adopting the forward model. The results indicated a significant association between cognitive anxiety (p = 0.001) and HRV. An increased magnitude of the association was observed when somatic anxiety was inserted in the model (p = 0.001). In contrast, self-confidence showed, which was inserted in block 3, no relationship with HRV (p = 0.27). It was concluded that cognitive and somatic anxieties were associated with the HRV of swimmers. Athletes with a high magnitude of cognitive and/or somatic anxiety demonstrated more significant autonomic nervous system disturbance. Practically, psychological interventions are needed to improve anxiety states that are specific to perform well, and to improve HRV.