How much different genders contribute to citations and whether we see different gender patterns between STEM and non-STEM researchers are questions that have long been studied in academia. Here we analyze the research output in terms of citations collected from the Web of Science of males and females from the largest Croatian university, University of Zagreb. Applying the Mann–Whitney statistical test, for most faculties, we demonstrate no gender difference in research output except for seven faculties, where males are significantly better than females on six faculties. We find that female STEM full professors are significantly more cited than male colleagues, while male non-STEM assistant professors are significantly more cited than their female colleagues. There are ten faculties where females have the larger average citations than their male colleagues and eleven faculties where the most cited researcher is woman. For the most cited researchers, our Zipf plot analyses demonstrate that both genders follow power laws, where the exponent calculated for male researchers is moderately larger than the exponent for females. The exponent for STEM citations is slightly larger than the exponent obtained for non-STEM citations, implying that compared to non-STEM, STEM research output leads to fatter tails and so larger citations inequality than non-STEM.