A cross-sectional study was conducted in Isiolo and Marsabit counties, Kenya to investigate the challenges associated with high camel calf mortality. Data were collected through focus group discussions and scheduled interviews. Milk pH levels were used to ascertain subclinical mastitis. Statistical analysis was performed through recurring themes, comparing means, and multiple linear regressions. The null hypotheses for the coefficients were rejected at the p < 0.05 significance level. Gross camel calf mortality was found to be 44.11%, with the most significant risk factors being predation, tick paralysis, and microbial diseases. Increasing the suckling period and the amount of milk consumed, along with short deworming intervals were associated with reduced morbidity and mortality from microbial diseases (p < 0.05). This is attributed to improved calf immunity. Subclinical mastitis was associated with a reduction in microbial diseases. Camel pox was positively associated with long intervals between treatments for external parasites because it is tick-transmitted. The study recommends prioritising calf rearing and implementing security measures to protect calves from predators. A longitudinal study is recommended to confirm whether the associations identified are the cause of the morbidities and mortalities observed.