Background: Vocal fold leukoplakia (VFL), despite our knowledge of its etiopathogenetic factors, and the development of laryngeal visualization, remains a diagnostic and therapeutic challenge. Objective: This research aimed to explore the efficacy of clinical and morphological feature identification in videolaryngoendoscopy (VLE) using a three-tier classification, and videolaryngostroboscopy (VLS) in predicting the risk of VFL malignant transformation. Material and Methods: We examined 98 patients with VFL by flexible endoscopy under VLE and VLS. Morphological characteristics of 123 lesions including the surface, margin, and texture were assessed; then, VFL was subdivided into three types: I—flat and smooth, II—elevated and smooth, and III—rough. Based on the histopathological findings, 76 (61.79%) lesions were classified as low- and 47 (38.21%) lesions as high-grade dysplasia. Results: The inter-rater agreement between two raters evaluating the VFL in VLE was almost perfect (Cohen’s kappa = 0.826; p < 0.00; 95% CI 0.748–0.904). In ROC curve analysis, the AUC difference between Rater I and Rater II was 0.024 (0.726 vs. 0.702). In multivariate analysis, high-risk VFL was positively related to unilateral plaque localization (p = 0.003), the type III VLE classification (p = 0.013), absence of a mucosal wave (p = 0.034), and a positive history of alcohol consumption (p = 0.047). In ROC analysis, VLE had an AUC of 0.726, with a high sensitivity of 95.7% and low specificity of 40.8%. The NPV was high, at 93.9%; however, the PPV was low, at 50%. The proposed logistic regression model including features significant in multivariate analysis showed lower sensitivity (80.9% vs. 95.7%) and lower NPV (86.2% vs. 93.9%); however, the specificity and PPV were improved (73.7% vs. 40.8% and 65.5% vs. 50.0%, respectively). Conclusions: The combination of clinical history with endoscopic (plaque morphology) and stroboscopic examination (mucosal wave assessment) can fairly estimate the degree of dysplasia in VFL and thus is recommended for use in clinical settings. The findings of this study can be used to guide the decision regarding immediate biopsy or watchful waiting.