Objective The aim of this study was to introduce a novel soft tissue thickness measurement method using cone beam computed tomography (CBCT) and to compare the new method with ultrasonic device applications and transgingival probing measurements. Methods Twenty-five participants (12 female, 13 male, age range, 25-51 years) were included the study. Soft tissue thickness in lateral incisor, canine, premolar, and molar regions were measured using transgingival probing (group T), ultrasonic device (group U), and CBCT scan measurements (group C). Differences and correlations between groups and agreement between measurement methods were evaluated. Results Soft tissue thickness was significantly lower in group U in premolar region, but was significantly higher in molar region compared with group C and group T (P < .05). There were significant positive correlations in lateral incisor and canine region, between group U and group C, in premolar region between group T and group C, and in molar region between group U and group C, and between group C and group T (P < .05). The highest agreement between measurement methods was evident between group T and group C. Conclusion Soft tissue thickness values in maxilla may differ depending on the measurement method and location of the measurement. Ultrasonic device, transgingival probing, and CBCT measures may not necessarily correlate in all locations. The high agreement between CBCT measurements and transgingival probing may suggest the newly introduced method as a promising technique for soft tissue thickness evaluation. Clinical Significance This study evaluated the relation between different soft tissue thickness measurement methods and demonstrated a novel method which can be used in any part of the mouth. The outcome also suggested that the measurement method and the location might affect the soft tissue thickness value obtained, and therefore might be important in clinical decision making.