This study aimed to investigate the effect of using high-quality colostrum in addition to paromomycin on the treatment outcomes and serum proteomes of calves naturally affected by cryptosporidiosis. Thirty Holstein calves infected with only Cryptosporidium spp. were divided into three equal groups. Calves in the PC group received paromomycin orally at a dose of 100 mg/kg once daily for 5 days. Calves in PCOL and PBCOL groups received 250 ml colostrum 3 h after feeding twice a day for 3 days. The PBCOL group was also given 6 g of sodium bicarbonate 15 min before colostrum administration. While the fecal scores of all calves were evaluated daily for 10 days from the initiation of the treatment, fecal oocyst counts were determined on the 0, 1, 2, 3, 5, 7, and 10th days. Brix%, total protein (TP), immunoglobulin G (IgG), gamma-glutamyltransferase (GGT) levels, and proteomic analyses were performed on the 0 and 3rd days' sera. Considering pretreatment values, fecal scores (8th, 2nd, and 2nd day), and fecal oocyst counts (10th, 3rd, and 2nd day) improved in a significantly (p < 0.05) shorter time in the colostrum groups than in the control group. By serum proteomic analysis, 99, 93, and 83 proteomes were detected in PC, PCOL, and PBCOL groups, respectively. Although the significant changes in any protein in Group PC were absent, significant changes were observed in Alpha-1B-glycoprotein (A1BG), Zinc transporterZIP11 (S39AB), Cathelicidin-1 (CTHL1), Actin_ cytoplasmic-1 (ACTB), and Apolipoprotein A-IV (APOA4) proteins in Group PCOL and Alpha-1-antiproteinase (A1AT), Serum amyloid A protein (SAA), Actin-cytoplasmic-2 (ACTG), Protein HP-20 homolog (HP20) proteins in Group PBCOL with colostral treatment, which indicated that the use of colostrum had an effect on calf serum proteomes. The more pronounced healing and shorter clinical improvement time in the colostrum groups especially colostrum with sodium bicarbonate revealed that these proteomes have positive effects in the treatment with their systemic and local effects in the intestines.