Two to five percent of infants and children experience febrile seizures (FS). Breastfeeding is beneficial to the health of mothers and children. Nevertheless, the benefits of breastfeeding in reducing FS remain unclear; thus, the present study aimed to evaluate this association. The case group was selected from 2010 to 2019, and the selected population was children younger than 5 years (i.e., children born from 2005–2019). The control group was selected from newborn infants at our hospital born between 2005 and 2019. Finally, 55 children with FS and 110 children in the control group were recruited. The results show longer breastfeeding duration is associated with an increased risk of FS (adjusted odds ratio: 1.06, 95% confidence interval: 1.01–1.11, p = 0.028). When comparing cases of FS with the control group, the percentage of inclusive breastfeeding over 12 months (32.7% vs. 9.1%, p = 0.017) and longer duration of exclusive breastfeeding were higher (10.86 ± 11.82 vs. 5.40 ± 7.17 months, p < 0.001). However, the comparison of the prevalence of FS between the different breastfeeding duration groups did not reach statistical significance. In conclusion, our study showed that a longer breastfeeding duration was associated with a higher risk of FS. Future large-scale studies evaluating the association between breastfeeding duration and febrile seizures are needed.