Campylobacter is the most common bacterial cause of foodborne illness globally. Both symptomatic and asymptomatic infections with Campylobacter species have been associated with growth faltering of children in low-resource settings, while previous prevalence studies primarily focused on diarrheal disease in children. Here, we leverage the data collected from the Campylobacter Genomics and Environmental Enteric Dysfunction (CAGED) project to characterize the spatial patterns of Campylobacter infections among infants with or without diarrhea in rural Eastern Ethiopia. Randomly enrolled infants (n = 106) were followed from birth to around 13 months, with fecal samples collected monthly. Livestock, drinking water, and soil samples were collected biannually. Campylobacter was detected and quantified using genus-specific PCR and species-specific PCR for four species. We employed a spatial filtering approach using genus-specific data to generate smoothed prevalence surfaces by month and age group. Temporally, an upward trend of prevalence was observed as the children grew older. Spatially, high-prevalence areas were distributed across the whole study area. To relate disease risk to environmental conditions, we used ecological niche modeling with MaxEnt to estimate habitat suitability of the genus Campylobacter and two dominant species identified by PCR results. Elevation, vegetation index, and slope were the most important contributors, and all distribution models suggested areas in the north were more likely to support the pathogen. These results inform Campylobacter infection patterns and identify target areas with higher risk of Campylobacter in low-resource settings. This further contributes to developing effective intervention strategies in the future.