Background Antioxidant and antihistamine agents from Barleria noctiflora L.f. as natural source due to the existing modern medicine give various adverse effects to overcome these problems with natural products. Methods B. noctiflora leaves extract was fractionated with column chromatography; the homogenized fractions were monitored with thin layer chromatography (TLC) and characterized by using UV–visible, FT-IR, 1 H NMR, 13 C NMR and mass spectrometry spectral studies. The volatile phytoconstituents of B. noctiflora extract were analysed by gas chromatography–mass spectrometry. Phytoconstituents from B. noctiflora leaves extract were screened for their antioxidant and antihistamine potential in vitro (2,2-diphenyl-1-picrylhydrazyl radical scavenging activity, 2,2′-azinobis-3-ethylbenzothiozoline-6-sulfonic acid radical decolouration assay, nitric oxide radical scavenging activity, superoxide radical scavenging activity and hydrogen peroxide radical scavenging activity) and in silico (molecular docking), respectively. Results Antioxidant and antihistamine barlerinoside has been isolated and characterized from the leaves of B. noctiflora L.f. Barlerinoside revealed their free-radical scavenging ability on OH − , OH • , NO − , O 2 − and H 2 O 2 radicals and found high percentage inhibition against OH − radical at the IC 50 value of 50.45±2.52 µg. The methanol (MeOH) extract of B. noctiflora leaves contains cyclotene; N,N-dimethylglycine; tetrahydrocyclopenta [1,3] dioxin-4-one; phenol, 2-methoxy-; benzofuran, 2-methyl-; 1,4:3,6-dianhydro-α- d -glucopyranose; 2-methoxy-4-vinylphenol; 1,3;2,5-dimethylene- l -rhamnitol; levoglucosan and bicyclo[2.2.2]oct-7-ene-2,5-dione as being the major compounds. Among phytoconstituents present in the extract, the hexestrol; 1,2-benzenedicarboxylic acid, bis(2-methylpropyl) ester; 1-(3,6,6-trimethyl-1,6,7,7a-tetrahydrocyclopenta[c]pyran-1-yl) ethanone; megastigmatrienone; furan interacted with histamine H 1 receptor and bind at GLU-177 and ASP-178 with high binding energy score −13.95, −13.41, −12.56, −12.03, and −11.72 kcal/mol, respectively, and the expected hydrolysed products of compound-1a and compound-1b from barlerinoside showed −8.91 and −8.68 kcal/mol binding energy against the histamine H 1 receptor. This showed that the active ligands exactly bind with active binding site of the protein. Conclusions We can conclude that isolated barlerinoside from B. noctflora L.f. has potent antioxidant activity against synthetic free radicals and antihistamine activity against histamine H 1 receptor.