External dacryocystorhinostomy (DCR) is the gold standard surgical technique for the treatment of primary acquired nasolacrimal duct obstruction (PANDO). However, new techniques such as endoscopic DCR and transcanalicular dacryocystorhinostomy (T-DCR) are being studied in an attempt to reduce surgical time, avoid external scarring and preserve the lacrimal pump while achieving the same efficacy. The purpose of this study was to compare the efficacy between conventional T-DCR and modified transcanalicular dacryocystorhinostomy (MT-DCR) in patients with PANDO. MT-DCR is performed to remove nasal mucosa prior to laser osteotomy. This is a comparative, prospective, interventionist and randomized study. Patients with PANDO were selected to undergo MT-DCR or T-DCR by blocked randomization. PANDO was diagnosed based on clinical presentation, dye disappearance test and dacryocystography. All of the procedures were performed by the same surgery team members. Anatomical success outcome was defined as positive lacrimal syringing and functional success outcome was defined as the absence or improvement of epiphora. A total of 44 surgical procedures were performed (22 MT-DCR and 22 T-DCR). In the case of MT-DCR, the anatomical and functional success rates after 12 months were 90 and 86%, respectively. After T-DCR, these rates were 77 and 72%, respectively (p = 0.162). MT-DCR and T-DCR are both safe and fast procedures with low morbidity and well-tolerated.