Burgeoning interest in marathons necessitates an understanding of performance determinants. Research has highlighted the importance of diet, training and sleep, yet relations of circadian preference and sleep inertia with marathon performance remain largely unexplored. Because marathons generally start early-to-mid morning, these characteristics may have relevant impact. This study investigates relationships of circadian preference, sleep inertia and their interaction with marathon completion time. Consenting participants in a 2016 large mass-participation city marathon completed self-report questionnaires capturing circadian preference and sleep inertia, along with demographics and other characteristics. Circadian preference and sleep inertia were described across subgroups. Analyses examined the associations and interactions of circadian preference and sleep inertia with marathon completion times, with adjusted analyses accounting for age, sex and sleep health. Participants were marathon finishers (n = 936; 64.5% male; 66.3% young-adults), with a majority reporting morningness tendencies (60.8%). Results supported a linear association between increasing eveningness preference with slower marathon times (p = 0.003; padjusted = 0.002), while some support was provided for a linear relationship between greater sleep inertia and slower marathon times (p = 0.04; padjusted = 0.07). A significant interaction was observed (p = 0.02; padjusted = 0.01), with the directionality suggesting that the circadian preference relationship weakened when sleep inertia severity increased, and vice-versa. Our results suggest deleterious associations of increasing eveningness preference and greater sleep inertia with marathon completion time. These features may aid identifying marathoners who could be at a disadvantage, while also serving as modifiable targets for personalized training regimens preceding competition.