Background Carbamazepine (CBZ) formed the gold standard drug in trigeminal neuralgia (TN) treatment but faces high therapeutic failure. This defined the need to explore a second line of drug therapy. The study aimed at comparing two alternate drugs i.e. Lamotrigine (LTG) and Pregabalin (PGB), in the management of TN refractory to therapeutic doses of CBZ. Methods Twenty-two patients with diagnosis of refractory TN were enrolled and randomly allotted into 2 groups of 11 each. Each group was subjected to a crossover analysis using LTG and PGB together with CBZ, for a period of 6 weeks. Patients maintained a pain diary, the scores of which, along with global evaluation scores, determined the primary outcome. Reevaluation of symptoms after 6 months was done to assess long term efficacy with study drugs. Results Both LTG and PGB were effective over CBZ alone (p \ 0.05); however, statistically insignificant difference (p [ 0.05) was observed between the two groups using Mann-Whitney tests. Unlike LTG, side effects like nausea, insomnia and concentration loss were minimal with PGB thus exhibiting greater patient compliance. Secondary analysis showed complete relief in 4 patients on PGB (mean dose 240.68 mg/day) while 6 had partial relief. Three patients on LTG (mean dose 310.90 mg/day) reported relapse of acute symptoms and required peripheral alcohol blocks. Conclusion Pregabalin has potential anti-neuralgia properties comparable to LTG. However, the level of patient's tolerance seen with PGB exceeds that with LTG. 6 months follow-up records suggest that PGB together with CBZ offers a more reliable pain control than with LTG.