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Paratuberculosis (Johne’s disease), caused by Mycobacterium avium subspecies paratuberculosis (MAP), is a chronic enteric infection that significantly impacts small ruminant health and productivity. Genetic variation in host immune genes, particularly SLC11A1, has been implicated in resistance to intracellular pathogens. The aim of this study was to investigate whether polymorphisms in the 3′UTR (GT)n microsatellite of SLC11A1 are associated with resistance or susceptibility to paratuberculosis in sheep, complementing existing SNP-based genome-wide association studies (GWAS) in cattle and goats. A total of 138 animals were genotyped, and a subset of 53 was analyzed for SLC11A1 expression. Six alleles were identified, with (GT)21 and (GT)23 significantly enriched in resistant sheep (p < 0.05), while (GT)22 and (GT)24 were more common in sensitive animals. Overall allele distribution showed a significant genotype–phenotype association (χ2 = 12.4, p = 0.006, Cramér’s V = 0.38). In contrast, no significant differences were observed in basal SLC11A1 mRNA expression between groups or across genotypes. Our findings extend previous GWAS results in sheep by providing preliminary allele-level resolution of a functional microsatellite locus. Identification of resistance-associated alleles provides a foundation for genetic selection strategies that complement vaccination and management, supporting sustainable control of paratuberculosis in sheep.