COVID-19 outbreak impacted negatively on teaching globally with traditional face-to-face teaching mostly affected. This study evaluated the experiences and perceptions of Nigerian undergraduate dental students to virtual learning (VL) including perceived institutional challenges during the COVID-19 pandemic. This was a cross-sectional survey of 346 dental students from all 13 Nigerian dental schools. Data collection was done using an open/close-ended online questionnaire. The level of awareness and understanding of dental students to virtual learning was high (93.6%) and good (84.7%), respectively. About two-thirds (62.4%) of the students had a virtual learning classroom experience before the COVID-19 pandemic. Clinical students spent more time on the Internet and reported more confidence in the use of VL platforms than their pre-clinical counterparts during the lockdown (p < 0.05). More male students than their female counterparts felt that VL had less quality than traditional classroom teaching (p < 0.05). Similarly, male students showed more confidence in the use of VL online tools (p < 0.05). Institutional and self-perceived preparedness to VL was ranked low and moderate by the students, respectively. The high cost of data subscriptions, unstable Internet connectivity, and lack of other institutional facilities were perceived as challenges to effective VL by students. None of the identified variables predict effective VL. Experiences of dental students and their preparedness to VL were moderate. The high cost of Internet subscriptions, unstable Internet connectivity, and low institutional facilities were major challenges to students' VL. None of the socio-demographic factors could successfully predict effective VL.