Growing evidence suggests that feeding practices in early childhood play a major role in the occurrence of childhood diarrhea. However, there is a lack of information regarding feeding practices and its relationship with occurrences of diarrhea in young children from Saudi Arabia. The present study is aimed to measure the prevalence of diarrhea and assess its relationship with feeding practices among children between two months and two years of age in Saudi Arabia. A cross-sectional study was carried out in two large cities in the Aseer region in southwest Saudi Arabia. A total of 302 mothers attending well-baby clinics across six primary health centers were included. A structured questionnaire was used to collect data. Factors associated with diarrheal disease were identified by multivariable logistic regression analysis. The prevalence of diarrhea among children during the study period was 56.3% (95% CI: 50.7%–61.8%). Only 15.9% of children in our study were exclusively breastfed. The occurrence of diarrhea was significantly associated with age 7–12 months (aOR = 2.64, 95% CI: 1.42–4.91). We found that diarrhea was prevalent among children between two months and two years of age, and that exclusive breastfeeding was not a common practice in this region. Health education programs should be directed towards mothers to improve rates of breastfeeding, weaning practices, food hygiene, and childcare. Special attention and support should be provided for working mothers.