Traditional management strategies of allergic rhinitis (AR) may show limited effectiveness and side effects. Intranasal injection of Botulinum toxin type A (BTX-A) and postganglionic parasympathectomy of pterygopalatine ganglion (PPG) are among the alternative treatment options of AR. In this study, we compared the efficacy of BTX-A and surgical parasympathectomy on treatment of uncontrolled AR. Sixty patients were recruited to the study who diagnosed with uncontrolled AR. Patients underwent either intranasal injection of BTX-A (Group A) or bilateral surgical parasympathectomy (Group B). All patients were evaluated in terms of nasal hypersecretions, congestion and sneezing with visual analogue scale prior to treatment and during the six months follow-up period. Nasal hypersecretions and sneezing were significantly differed in both groups before and after the interventions. The significant efficacy on sneezing was documented in both groups in the first 4 and 8 weeks, respectively. The efficacy on nasal hypersecretions extended for 12 weeks in group A and  throughout the follow-up period in group B. Nasal congestion did not differ in both groups. In patients with uncontrolled AR, BTX-A and surgical parasympathectomy, may be a long-lasting therapeutic option for the treatment of nasal hypersecretions, but not for sneezing and nasal congestion.