Pentadesma butyracea is a medicinal plant of which stem bark decoctions are used in traditional medicine for the treatment of diarrheal in Gabon. The aims of the present work were to perform a phytochemical analysis of P. butyracea stem bark decoctions harvested in rain and dry seasons and to evaluate their biological proprieties in order to improve their pharmaceutical use. In a first approach, spectrophotometric analyses were used to quantify phenolics compounds, following by liquid chromatography coupled to mass spectrometry analysis that allowed the identification of flavanone-flavone dimers as the main metabolites of this stem bark decoction. Pharmacological analyses showed the absence of in vitro and in vivo toxicity, thus allowing the safety in use of this decoction. The antioxidant activity of the samples was also demonstrated. Of particular interest, the decoction of P. butyracea stem barks exhibited in vitro antidiarrheal activities thanks to the effects on contractions of ileum fragments isolated from rats. In addition, in vivo activities on castor oil-induced diarrhea in rats were also demonstrated. These results encourage the deepening of a bio-guided research on P. butyracea stem bark decoctions in order to propose standard traditional medical treatments in Gabon.