Aims: This study aimed to compare central corneal thickness (CCT) using ultrasound pachymetry (USP) (CCT apex) and specular microscopy (CCT vertex) and also to find out the intra-reading variability from the two instruments. Settings and Design: A prospective, observational study was conducted in a tertiary eye care center in southern India. Materials and Methods: This study was conducted on 12 patients (24 eyes, 96 data set eyes, 768 data points in total) aged 20–50, in non-pathological corneas. Eight CCT measurements by specular microscopy and eight measurements by USP were taken by two different experienced observers on day 1, followed by repeating the same on day 2. Statistical Analysis: The readings were averaged and compared by paired t-test. SPSS software was used for statistical analysis. Variability between the eight readings produced by the same instrument was calculated and coefficient of variation was plotted. Inter-examiner variability and intra-examiner variability of the two modalities were studied, and it was considered statistically significant if P < 0.05. Results: The mean CCT by USP was 522.71 µm and the mean CCT by specular microscopy was 519.43 µm. The coefficient of variation of the eight readings varied significantly between the machines. On an average, the coefficient of variation was 0.4% compared to 0.8% in specular microscopy and USP, respectively. Conclusion: The intra-reading variability of ultrasound CCT is twice as that compared to specular microscopy. The clinical relevance of this spread is relevant and important in modern-day practice. Hence, it is better advisable that CCT readings from both the modalities, not be used interchangeably.