Calf morbidity is an important productivity factor that results in huge economic losses in the success of livestock production in Ethiopia. However, there is no robust information on its rate and its predictors in the mixed crop livestock production system as most studies are targeted to intensive dairy farms. A longitudinal study design was conducted from December 2018 to April 2019 in Siyadeber and Wayu districts of Amhara region, Ethiopia. A total of 135 apparently healthy calves were enrolled from randomly selected fifty-fifty households in three Kebeles of the district, namely, Gash-amba, Siyadeber, and Wale-deneba. A pretested structured questionnaire was used to collect data about the potential risk factors upon the face-to-face interview made with the owners. Calves were monitored for the incidence of morbidity in a weekly visit basis, and any clinical abnormalities were recorded on registries. The chi-square and Fisher’s exact test followed by Generalized Linear Models for binomial family extensions for risk estimate were run, and a p value <0.05 was considered statistically significant. In this study, the overall incidence rate of calf morbidity among under six months of age was 388 calves per 100,000 days of follow-up, with a cumulative incidence of 34.1% (95% CI: 26.1–42.7). Calf diarrhea, pneumonia, septicemia, dehydration, and navel ill were the encountered health problems consecutively. Among the potential risk factors, calves from Siyadeber Kebele (RR = 2.11, 95% CI: 1.13–3.94), calves housed with other livestock (RR = 2.05, 95% CI: 1.10–3.80), housed with their dam (RR = 1.92, 95% CI: 1.20–3.05), without bedding (RR = 1.89, 95% CI: 1.20–2.94), and calves whose dam age ranges from 5 to 8 years (RR = 1.87, 95% CI: 1.05–3.35) were found to be predictors of calf morbidity. In general, the high calf morbidity rates established in this study together with the alarming predictors of calf morbidity entail attention by the concerning bodies on proper management and improved health care so as to reduce the calf morbidity.