As it stands, the diagnosis of non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP) is primarily based on histological analysis. We hypothesised that computerised analysis of nuclear images of cytological specimens could be used to differentiate NIFTP from papillary thyroid carcinoma follicular subtype (PTCFS) and follicular carcinoma (FC), influencing patient management. We employed a retrospective analytical observational study based on nuclear morphometric variables of cytological material from thyroid nodules classified as PTCFS, NIFTP, or FC. Five cases of each entity were analysed. Cytological slides were photographed, and 1170 cells for each entity were analysed digitally. The captured images were evaluated (blindly) using the ImageJ software package. The morphometric evaluation included area, perimeter, width, height, and circularity. Numerical variables were expressed as mean, median, minimum, and maximum (min; max) values. Kruskal-Wallis and Dunn's tests were used with a 5% significance level. Regarding nuclear analysis, all variables differed among the three groups (p < 0.001). Given the interdependence among the variables, these data indicated that nuclear size was greatest in the NIFTP group, followed by FC and PTCFS. Our analysis of the digital images, with a focus on nuclear parameters, found significantly difference among cytological specimens from cases of NIFTP, PTCFS and FC. Thus, this tool has the potential to provide additional information that may help in the diagnosis of NIFTP, even during the preoperative period. Additional studies are needed to create protocols, evaluate the applicability of nuclear morphological and morphometric parameters-focusing on digital pathology-and create algorithms and tools to assist cytopathologists with their diagnostic routines.