Toll-like receptor 1 (TLR1) recognises lipopeptides with TLR2, and affects immune response to Mycobacterium tuberculosis infection. Here, we report results of the first case-control paediatric study of the TLR1 single-nucleotide polymorphisms and susceptibility to tuberculosis (TB). A paediatric case-control study enrolled 340 TB patients and 366 healthy controls, all Han Chinese from North China. Significant differences of the allelic and genotypic distributions of rs5743618 in TLR1 gene were observed between TB group and control group and, G allele of rs5743618 was associated with increased risk for TB (OR: 2.40, 95% CI: 1.41–4.07, p = 0.0009). In addition, after stimulated with inactivated lysate of Mycobacterium tuberculosis strain H37Rv, whole blood samples from children with the rs5743618 GT genotypes showed a decreased level of Interleukin-12p40 (IL-12p40), Tumour Necrosis Factor-a (TNF-a) and CXC chemokine ligand 10 (CXCL10) production. To conclude, TLR1 rs5743618 G allele was found associated to susceptibility to TB in Han Chinese paediatric population. TLR1 rs5743618-GT genotype carriers may have reduced immune response to MTB infection although further study is warranted to test this conclusion.