Crocodilians exhibit continuous tooth replacement (i.e., polyphyodonty) and have been identified as suitable models for tooth regeneration research due to the similarity in dental cavity and tooth anatomy between these creatures and humans. Various studies reporting in ovo bird embryo manipulation exist, but such reports for reptiles are virtually non-existent. Egg windowing enables direct access to oviparous vertebrate embryos and is therefore an important component of in ovo embryo manipulation experiments. The aim of the present study was to window Nile crocodile, Crocodylus niloticus eggs and assess the potential of direct manipulations, targeting the pharyngeal region where the maxilla and mandible originates. Crocodylus niloticus eggs were successfully windowed, and a limited number of individuals survived the entire gestation period. The 1st trimester of gestation was the most sensitive, and 96.78% of the mortalities occurred within this period. Our data indicate the suitable window for embryo manipulation targeting the mandibular arch and maxillary process, without a risk of damaging the chorioallantoic membrane (CAM) (which may be fatal), was between day six and eight after laying for embryos incubated at 31°C. This data will be of use for future embryo-based experiments related to jaw and tooth development in crocodiles as well as human tooth regeneration research.