Polycystic ovary syndrome (PCOS) is the most common endocrine disorders in women of reproductive age, whose lifestyle approach is an essential part of the treatment. Recently, chronotype, i.e., a trait that determines individual’s circadian preference in behavioral and biological rhythms, has been reported to play a role in determining nutrition preferences and the risk of developing chronic diseases. Thus, the aim of this study was to investigate if chronotype categories (morning, evening, and neither) could be used as tool to screen eating habits in women with PCOS. In this observational cross-sectional study, we assessed anthropometric measurements, lifestyle habits, chronotype categories, adherence to the Mediterranean Diet, dietary pattern, and metabolic parameters in 112 women with PCOS. Chronotype was classified as morning in 27.7%, evening in 42.9%, and neither in 29.5% of subjects. Women with PCOS with evening chronotype showed significantly higher percentages of grade I (p = 0.003) and grade II obesity (p = 0.001), did less regular exercise (p < 0.001), and most of them were smokers (p < 0.001) compared to those with neither and morning chronotypes. Women with PCOS with evening chronotype were significantly more insulin resistant (Homeostatic Model Assessment of Insulin Resistance (HoMA-IR) cut off > 2.5) than other two chronotypes (p < 0.001). Women with PCOS with evening chronotype had the lowest PREvención con DIetaMEDiterránea (PREDIMED) score, consumed more calories (p < 0.001), total (p < 0.001) and simple carbohydrates (p < 0.001), total fat (p < 0.001) and saturated fatty acids (p < 0.001), polyunsaturated fatty acids (p < 0.001) and n-6 polyunsaturated fatty acids (p < 0.001), and less fiber (p < 0.001) than women with PCOS with other chronotypes. In addition, women with PCOS with evening chronotype consumed less extra virgin olive oil (p = 0.001), legumes (p = 0.038), fish/seafood (p < 0.001), and tree nuts (p = 0.041) than women with PCOS of the other two chronotype categories and less red wine (p < 0.001) and more red/processed meat (p < 0.001) than women with PCOS with morning chronotype. In conclusion, in women with PCOS, evening chronotype has been associated with a most severe insulin resistance and unhealthiest eating habits. Thus, chronotype assessment could be an effective tool to screen the eating habits, and more generally the lifestyle, of women with PCOS.