The aim of the present study was to examine the effect of place of residence on physical fitness and adherence to Mediterranean Diet (AMD) in 3–5-year-old children, i.e., whether those who live in urban areas differ than those in rural and whether any difference varied by age. Participants were 363 preschoolers (age 3–5 years old), who performed a series of anthropometric, physical fitness tests and measured their nutritional habits through a 16-item Mediterranean Diet (KIDMED) questionnaire. The main findings of the present study were that (a) boys had better performance in ball bouncing, Medicine Ball Throw Test (MBTT), 25 m sprint, Standing Broad Jump (SBJ), crawling, and shuttle run test (SRT) than girls, and the magnitude of these differences was small; (b) preschoolers in urban residence were taller than those in rural and had better performance in SRT; (c) older preschoolers had larger anthropometric characteristics and better performance than younger preschoolers; (d) the magnitude of the effect of age was larger than the effect of residence; and (e) good AMD was more prevalent in boys than in girls and in 3-year-old participants than in their older peers, but was not related to place of residence. Therefore, these findings identified the need to develop exercise and nutrition intervention programs in preschoolers considering sex, age, and place of residence.