There is a knowledge gap on colistin-resistant and mobilized colistin-resistant (mcr) Escherichia coli in sheep and goats worldwide. This study determined the prevalence and antimicrobial resistance of mobilized colistin-resistant (mcr) E. coli in dairy sheep and goat flocks in Jordan. A total of 948 milk samples were collected from 155 flocks across Jordan. The milk samples were pre-enriched in MacConkey broth and then plated on MacConkey agar supplemented with 8 mg/l colistin and the presence of mcr-1 gene in the isolates was tested by polymerase chain reaction. In total, 1,158 E. coli isolates were colistin resistant, with 74.8% herd-level prevalence and 39.5% individual animal prevalence. Sixty-one (5.3%) of 1,158 phenotypically colistin-resistant E. coli harbored mcr-1, with 23.9% herd-level prevalence and 6.6% individual animal prevalence. About 77.1% of the mcr-1 E. coli resisted one or more antimicrobial classes and 37.7% were multidrug resistant. More than 30% of the mcr-1 positive E. coli isolates were resistant to nalidixic acid, tetracycline, ceftazidime, cefpodoxime and ampicillin, whereas 8–20% of the isolates were resistant to cefotaxime, ceftriaxone, gentamicin, tobramycin, sulfamethoxazole-trimethoprim, and amoxicillin-clavulanic acid. This study indicates that small ruminants are reservoirs of colistin-resistant and mcr-1 positive E. coli that exhibit co-resistance to critically important antimicrobials which would pose public health issue and calls for the necessary banning of the use of colistin in small ruminants.