Abstract Background Hemophilia B (HB) is a coagulation disorder with an X‐linked recessive inheritance pattern, caused by plasma FIX deficiency. In Colombia, HB is considered a rare and high‐cost disease, with 362 males reported in 2017. Methods Here, we characterized 20 HB apparently unrelated families by PCR amplification and Sanger sequencing. Results Fourteen unique variants were identified: seven missense, three nonsense, one variant in the 3′ UTR region, two large deletions >50 bp, and one intronic substitution that affects splicing c.520+13A>G that was present in 7/20 patients (35%). All these variants have been previously reported in the literature, except for exons 3 and 4, deletions, present in one patient. The genotype‐phenotype association correlates with the reported in the literature, with the exception of one patient. Conclusion This molecular analysis allowed us to establish the causal variant of HB in 100% of patients, to provide the appropriate genetic counseling to each of the families, and to propose a more cost‐effective carrier analysis. Here, we reported the first variants in Colombian population with Hemophilia B, finding a new variant and one intron recurrent variant present in 35% of patients.