(1) Background: The process of managing children at the emergency dental clinic (ER-C) is a difficult challenge. This matched case-control study assessed risk factors associated with children visiting the ER-C compared to visits at the regular dental clinic (RD-C). (2) Methods: The participants included 421 children aged three to 12 years who were recruited at the ER-C (cases) and RD-C (controls) at King Abdulaziz University Dental Hospital, with each group matched for gender and age. A data-collection form was developed and validated in both Arabic and English, containing the following four sections: DMFT/dmft index, Frankl’s behaviour rating scale, Dental Neglect Scale, and Dental Care Barriers questionnaire. (3) Results: The ER-C (vs RD-C) group showed significantly more uncooperative behaviour (p = 0.002), a higher total mean dental neglect score (p = 0.003), and a higher dental barrier score (p < 0.001). Binary regression analysis showed that those making their first visit (AOR: 2.65, p < 0.001) and with higher dental barriers (AOR: 1.121, p < 0.001) were statistically significantly more associated with ER-C visitation. (4) Conclusion: These findings suggest that children who visit the ER-C are more prone to dental care barriers, uncooperative behaviour, and dental neglect, thus highlighting the importance of encouraging and planning their attendance to ensure optimal dental care.