Sex has been recognized to be an important indicator of physiological, psychological, and nutritional characteristics among endurance athletes. However, there are limited data addressing sex-based differences in dietary behaviors of distance runners. The aim of the present study is to explore the sex-specific differences in dietary intake of female and male distance runners competing at >10-km distances. From the initial number of 317 participants, 211 endurance runners (121 females and 90 males) were selected as the final sample after a multi-level data clearance. Participants were classified to race distance (10-km, half-marathon, marathon/ultra-marathon) and type of diet (omnivorous, vegetarian, vegan) subgroups. An online survey was conducted to collect data on sociodemographic information and dietary intake (using a comprehensive food frequency questionnaire with 53 food groups categorized in 14 basic and three umbrella food clusters). Compared to male runners, female runners had a significantly greater intake in four food clusters, including “beans and seeds”, “fruit and vegetables”, “dairy alternatives”, and “water”. Males reported higher intakes of seven food clusters, including “meat”, “fish”, “eggs”, “oils”, “grains”, “alcohol”, and “processed foods”. Generally, it can be suggested that female runners have a tendency to consume healthier foods than males. The predominance of females with healthy dietary behavior can be potentially linked to the well-known differences between females and males in health attitudes and lifestyle patterns.