Nomophobia is the discomfort caused by not being in contact with a cell phone. Few studies have addressed nomophobia in university students. The study aimed to evaluate nomophobia and its associated factors in Peruvian medical students. We conducted an analytical cross-sectional study on Peruvian medical students between June 2020 and March 2021, using an online survey disseminated through social networks. We analyzed 3139 responses (females: 61.1%, median age: 22 years): 25.7% presented moderate nomophobia and 7.4% severe nomophobia. In the adjusted model, the nomophobia score was lower in students ≥24 years (β: −4.1, 95% CI: −7.2 to −1.0) and was higher in those who had a mobile internet data plan (β: 2.9, 0.8 to 5.0), used the cell phone >4 h (β: 4.5, 2.3 to 6.7), used a smartphone mainly for education (β: 2.5, 0.2 to 4.8), social networks (β: 8.2, 5.8 to 10.6) and entertainment (β: 3.3, 0.5 to 6.1), and those who presented possible anxious (β: 6.6, 4.3 to 8.9) or depressive (β: 19.5, 5.2 to 9.6) symptomatology. In conclusion, nomophobia in university students is a frequent and emerging problem, present mainly at younger ages and associated with symptoms of anxiety or depression. Implementing evaluation and early intervention strategies would favor the mental health of university students.