(1) Background: Assessing phonatory disorders due to laryngeal biomechanical alterations requires aerodynamic analysis, assessing subglottic pressure, transglottic flow, and laryngeal resistance. This study explores whether the acoustic parameter, the relative fundamental frequency (RFF), can be studied using the current acoustic analysis protocol at the University of Navarra’s voice laboratory and its association with pathologies linked to laryngeal biomechanical alterations. (2) Methods: A retrospective cohort study included patients diagnosed with muscular tension dysphonia, organic lesions of the vocal fold, and vocal fold paralysis (VFP) at the Clínica Universidad de Navarra from 2019 to 2021. Each patient underwent endoscopic laryngeal exploration, followed by acoustic study, RFF calculation, and an aerodynamic study. Additionally, a control group was recruited. (3) Results: 79 patients and 22 controls were studied. Two-way ANOVA showed significant effects for groups and cycles in offset and onset cycles. Statistically significant differences were observed in cycle 1 onset among all groups and in cycles 1 and 2 between the control group and non-healthy groups. (4) Conclusions: RFF is a valuable indicator of phonatory biomechanics, distinguishing healthy and pathological voices and different disorders. RFF in onset cycles offers a cost-effective, accurate method for assessing biomechanical disorders without complex aerodynamic analyses. This study describes RFF values in VFP for the first time, revealing differences regardless of aerodynamic patterns.