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The in vitro activity of <i>L. donovani</i> (promastigotes, axenic amastigotes and intracellular amastigotes in THP1 cells) and <i>T. brucei</i>, from the fractions obtained from the hydroalcoholic extract of the aerial part of <i>Hypericum afrum</i> and the isolated compounds, has been evaluated. The chloroform, ethyl acetate and <i>n</i>-butanol extracts showed significant antitrypanosomal activity towards <i>T. brucei</i>, with IC₅₀ values of 12.35, 13.53 and 12.93 µg/mL and with IC₉₀ values of 14.94, 19.31 and 18.67 µg/mL, respectively. The phytochemical investigation of the fractions led to the isolation and identification of quercetin (<b>1</b>), myricitrin (<b>2</b>), biapigenin (<b>3</b>), myricetin (<b>4</b>), hyperoside (<b>5</b>), myricetin-3-<i>O</i>-β-<span style="font-variant: small-caps;">d</span>-galactopyranoside (<b>6</b>) and myricetin-3’-<i>O</i>-β-<span style="font-variant: small-caps;">d</span>-glucopyranoside (<b>7</b>). Myricetin-3’-<i>O</i>-β-<span style="font-variant: small-caps;">d</span>-glucopyranoside (<b>7</b>) has been isolated for the first time from this genus. The chemical structures were elucidated by using comprehensive one- and two-dimensional nuclear magnetic resonance (1D and 2D NMR) spectroscopic data, as well as high-resolution electrospray ionization mass spectrometry (HR-ESI–MS). These compounds have also been evaluated for their antiprotozoal activity. Quercetin (<b>1</b>) and myricetin (<b>4</b>) showed noteworthy activity against <i>T. brucei</i>, with IC₅₀ and IC₉₀ values of 7.52 and 5.71 µM, and 9.76 and 7.97 µM, respectively. The <i>T. brucei</i> hexokinase (TbHK1) enzyme was further explored as a potential target of quercetin and myricetin, using molecular modeling studies. This proposed mechanism assists in the exploration of new candidates for novel antitrypanosomal drugs.