Background: Antimicrobial resistance (AMR) is a global health crisis, driven partly by inappropriate antibiotic use. In Nigeria, malaria remains highly prevalent and often mismanaged with antibiotics, particularly in presumed malaria-typhoid co-infections. This study examined patterns of antibiotic use in malaria treatment among university students, highlighting implications for AMR. Methods: A cross-sectional survey was conducted among undergraduates purposively selected from 12 universities across Nigeria’s six geopolitical zones. Data were collected via validated online questionnaires (February–March 2025) and analysed using descriptive statistics, chi-square tests, logistic regression, and Spearman correlation (SPSS v26). Results: Of 646 respondents, > 97% demonstrated general antibiotic knowledge, yet 27.6% misidentified chloroquine as an antibiotic. While 94.6% correctly recognised antibiotics for bacterial infections, about one-fifth believed they were effective against fungal, parasitic, or viral diseases. Despite 84.7% AMR awareness, 49.1% reported using antibiotics for malaria treatment. Misuse was highest in the Northeast (62.3%), Northwest (63.7%), and South-South (32.9%). In the Northeast, key drivers included prior experience (35.4%), pharmacist advice (29.9%), and peer influence (28.0%), while only 6.7% followed physician prescriptions. Misuse correlated with the belief that antibiotics treat all illnesses (rs = 0.329, p < 0.001). Nearly half (49.5%) accessed antibiotics without prescriptions. Conclusions: High AMR awareness contrasts with persistent misuse of antibiotics for malaria, reflecting misconceptions, regional disparities, and weak regulation. Targeted education, stricter antibiotic controls, and improved diagnostics are urgently needed to curb AMR in Nigeria.