BackgroundThe aim of the present study was to compare the effects on vertical dentoskeletal dimension produced by Pendulum appliance and Clear Aligners in patients with Class II malocclusion.Trial designThis is a prospective two-arm parallel group randomized clinical trial with 1:1 allocation ratio.MethodsThe Pendulum Group (PG) consisted of 20 patients (15F, 5 M) with a mean age of 17.2 ± 4.3 years. The Clear Aligners Group (CAG) comprised 20 patients (13F, 7 M) with a mean age of 17.2 ± 3.2 years. Distalization’s protocol in PG involved the activation of TMA wires till the achievement of Class I molar relationship. A protocol of sequential distalization was applied in the CAG. For each subject lateral cephalograms have been analyzed before treatment (T1) and at the end of the therapy (T2). Descriptive statistics and statistical between-group comparisons (PG vs CAG) were calculated for the craniofacial starting forms at T1 and for the T2–T1 changes. Statistical between-group comparisons for the T2–T1 changes were performed with independent samples t-tests (P < 0.05).ResultsThe PG showed significantly greater increases in SN^GoGn° when compared with CAG (+ 2.1 and − 0.3 degrees, respectively). Clockwise rotation of the occlusal plane with significantly greater increase of SN^POccl angle was observed in PG (+ 2.8 degrees) when compared with CAG (− 4.2 degrees).The PG revealed a significant increase in the N-Me variable with a mean change of + 4.4 mm compared to the CAG with mean values of − 1.2 mm. The PG showed an increase in the ArGo^GoMe angle (+ 0.7° degrees) compared to the CAG (− 3.4° degrees). The PG showed significantly greater increases in both maxillary and mandibular first molar to palatal plane (+ 1.3 and + 2.1 mm, respectively) when compared with CAG (− 0.9 and − 0.2 mm, respectively).ConclusionsUpper molar distalization with clear aligners represents a valid alternative to non-extraction treatment of Class II malocclusion, reducing the extrusion of maxillary first molars and improving the management of the occlusal plane and vertical dimension.Trial registration: ClinicalTrials.gov, NCT05298280. Registered 28 March 2022—Retrospectively registered, https://clinicaltrials.gov.