This study looked to assess the stability of Cryptosporidium parvum genotypes in calves between the final day of treatment with the antiprotozoal halofuginone lactate and seven days post-treatment. Paired faecal samples were collected on the final day of treatment and seven days later from 54 calves across seven farms in South-west England. The presence of Cryptosporidium species was detected using polymerase chain reaction targeting the 18 s rDNA. The presence and genotype of C. parvum was determined by PCR and amplicon sequencing targeting the gp60 locus. On farms where C. parvum was detected at both sampling times there was a distinct genotype shift. Detection of gp60 genotype IIaA15G2R1 decreased from 40% to 7% while IIaA17G1R1 increased from 0% to 41%, supplemented by IIaA16G3R1 in one sample. A shift in C. parvum genotypes present in calves within a one week sampling timeframe has not been described prior to this study, indicating that the timeframe is likely suitable for observing variation in C. parvum populations and interactions with antiprotozoal control strategies.