Background: Allergic rhino-conjunctivitis (AR) is a common disorder in children, which causes significant morbidity and impact on learning and day-to-day activities. Objectives: To compare effectiveness of montelukast versus cetirizine in AR and its effect on the quality of life (QoL) among children aged 6-12 years, attending Asthma Clinic, Faculty of Medicine, University of Ruhuna, Sri Lanka. Method: This was a randomized, double-blind, parallel-group trial; 'Group A' was given montelukast with a cetirizine dummy; 'Group B' was given cetirizine with a montelukast dummy. Primary endpoint was to compare improvement of nasal, eye and night symptom scores. Secondary endpoint was to compare the QoL between the groups. Total symptoms were assessed at baseline, one month, two months and three months. Results: There were 176 children (62.5% boys) with a mean age of 8.82 ± 1.79 years. Fifteen children were lost to follow-up, 7 from the montelukast and 8 from the cetirizine group. There was a significant reduction in all symptoms (p<0.05) every month in both treatment groups. Whilst montelukast group had more improved day and night symptom scores than cetirizine group, statistically significant improvement was seen only in the 3rd month (t-4.10 p <0.001). Mean QoL score showed no significant difference between the two groups at onset (montelukast 9.01±9.4 and cetirizine 15.9 ± 10.4; t-0.369; p=0.712). Both groups showed a statistically significant improvement in all domains of QoL by completion of treatment (p<0.05). Upon completion, the montelukast group showed a significantly better QoL than the cetirizine group. Conclusions: Both cetirizine and montelukast showed remarkable improvement in the symptoms and better QoL in children. Study outcomes in all clinical domains and QoL were more significantly improved in montelukast group than in cetirizine group when treatment was continued for 3 months.