Whiplash injury is an initiating or aggravating factor of temporomandibular disorder (TMD). Although there are sex‐related differences in the mechanism of pain perception and pain control, there is a lack of research on differences in TMD after whiplash injury. We aimed to evaluate sex‐related differences in the clinical symptoms and magnetic resonance imaging (MRI) findings of patients with TMD attributed to whiplash injury. This retrospective, cross‐sectional study included 100 patients (50 women; 50 men; mean age, 37.60 years) who visited our oro‐facial pain clinic with symptoms of TMD after whiplash injury. All patients underwent detailed evaluations for history of trauma, and their clinical and MRI findings were comprehensively assessed. Women with TMD after whiplash injury perceived more pain and presented more tenderness upon palpation than did men with TMD. In addition, women showed higher volume (58% vs 26%) and signal changes (54% vs 20%) in the lateral pterygoid muscle (LPM) and more anterior disc displacement without reduction (ADDWoR) (40% vs 20%) than did men. The presence of ADDWoR (odds ratio, 10.58; P = 0.007) and condylar degeneration (odds ratio, 9.30; P = 0.015) predicted LPM volume; stressful conditions (beta = 1.34; P = 0.011) correlated with increased visual analogue scale scores, and sleep problem was associated with an increased palpation index (PI) (beta = 0.42; P < 0.001) and neck PI (beta = 0.49; P < 0.001) scores only in women. Our results showed sex‐specific differences in pain intensity, distribution of clinical and abnormal MRI findings, and their relationships, and these differences should be considered when treating patients with TMD.