•A previously undescribed peptide (Cl13) was obtained from C. limpidus scorpion venom.•The amino acid sequence and function were determined.•It contains 66 amino acids, 4 disulfide bonds and functions as a β-SCTx.•Cl13 affects mainly the human voltage dependent sodium channels 1.4, 1.5 and 1.6.•Antibody fragments specific for Cll1m and Cll2 do not recognize Cl13. A previously undescribed toxic peptide named Cl13 was purified from the venom of the Mexican scorpion Centruroides limpidus. It contains 66 amino acid residues, including four disulfide bonds. The physiological effects assayed in 7 different subtypes of voltage gated Na+-channels, showed that it belongs to the β-scorpion toxin type. The most notorious effects were observed in subtypes Nav1.4, Nav1.5 and Nav1.6. Although having important sequence similarities with two other lethal toxins from this scorpion species (Cll1m and Cll2), the recently developed single chain antibody fragments (scFv) of human origin were not capable of protecting against Cl13. At the amino acid sequence level, in 3 stretches of peptide Cl13 (positions 7–9, 30–38 and 62–66) some differences with respect to other similar toxins are observed. Some of these differences coincide with contact points with the human antibody fragments.