Ceiba pentandra (L.) Gaertn. (Bombacaceae) is popular for the quality of its wood. However, its leaf, stem bark and root bark have been popular in ethnomedicine and, apart from the inflorescence, have been subject of extensive phytochemical investigations. In this study, two compounds were isolated from the crude methanol extract of the inflorescence. Through data from UV, NMR, MS, electrochemical studies, differential scanning calorimetry, and thermogravimetric analysis, the structures were elucidated as 3-C-β-d-glucopyranosyl-1,3,6,7-tetrahydroxyxanthone (1) and 2-C-β-d-glucopyranosyl-1,3,6,7-tetrahydroxyxanthone (mangiferin, 2). They were assessed for antioxidant efficacy (DCFDA assay) and for anti-inflammatory efficacy using the lipopolysaccharide (LPS)-induced inflammation model in the RAW 264.7 macrophages (nitrite levels quantified, using Griess Assay, as surrogate for nitric oxide (NO)). Compound 1 (named ceibinin) was established as a novel positional isomer of mangiferin (2). While both 1 and 2 were antioxidant against basal and hydrogen peroxide (100 μM)-induced oxidative stress (6.25 μg/ml abrogated peroxide-induced oxidative stress), ceibinin (1) demonstrated no anti-inflammatory potential, unlike mangiferin (2) which, as previously reported, showed anti-inflammatory effect. Our work reports a positional isomer of mangiferin for the first time in C. pentandra and demonstrates how such isomerism could underlie differences in biological activities and thus the potential for development into therapeutics.