Background: Human African trypanosomiasis is one of the most serious neglected tropical diseases causing fatal symptoms and death. Natural products are a main source for anti-infective metabolites. Objectives: The objective of the study is to evaluate eight different plants belonging to the Kalanchoe species growing in Egypt for antitrypanosomal, antimalarial, antileishmanial, cytotoxic, and antimicrobial activities. Materials and Methods: The antitrypanosomal activity against Trypanosoma brucei; cytotoxic activities against human colon carcinoma, human hepatocyte carcinoma, and human breast adenocarcinoma cell lines; antileishmanial activity against Leishmania donovani; antimalarial activity against Plasmodium falciparum; and antimicrobial activities of all plant extracts have been examined. As well as the identification of the secondary metabolites for the most active extract was performed via ultra performance liquid chromatography coupled to high resolution quadrupole time of flight mass spectrometer operated in negative and positive ionization modes. Results: Among the examined plant extracts, Kalanchoe longiflora leaves extract showed promising activity against T. brucei with an inhibition concentration of sample at 50% fall in absorbance (IC50) value of 17.6 μg/mL. K. longiflora with other extracts exhibited promising cytotoxic activities. Profiling of the polar secondary metabolites of K. longiflora revealed the presence of 47 metabolites including 31 flavonoids, 9 phenolic acids, 4 anthocyanidins, 2 chalcone glucoside, and 1 coumarin. To determine the mechanism of action of K. longiflora extract as a potent antitrypanosomal and cytotoxic agent, we investigate its ability to inhibit topoisomerase I enzyme. K. longiflora extract showed an excellent activity with an IC50 value of 0.148 μg/mL. Conclusion: These interesting results open the door for further research aiming at the development of a successful treatment for Trypanosoma from K. longiflora.