Objective This study aimed to evaluate the accuracy of linear measurements made on cone beam computed tomography (CBCT) (New Tom VGi) scans with different image magnifications. Methods Forty-two titanium pins were inserted into seven dry sheep mandibles. Lengths of the pins were measured using a digital caliper with 0.01 mm readability, and the mandibles were radiographed using a CBCT unit. After reconstruction of CBCT images, three experienced radiologists measured the length and diameter of titanium pins at 100%, 200% and 400% magnifications. Accuracy of measurements was analyzed using descriptive statistics and one-way analysis of variance. P < 0.05 was considered statistically significant. Interobserver reliability was calculated using the intraclass correlation coefficient test. Results The mean differences of linear measurements from the actual lengths of pins were 0.1960, 0.2143 and 0.2047 mm at 100%, 200% and 400% magnifications, respectively (P > 0.05). The mean differences of linear measurements from the actual diameters of pins were 0.2206, 0.2063 and 0.1984 mm at 100%, 200% and 400% magnifications, respectively (P > 0.05). Interobserver reliability of pin length measurements was estimated to be 0.285, 0.707 and 0.479 at 100%, 200% and 400% magnifications, respectively. Interobserver reliability of pin diameter measurements was 0.078, 0.469 and 0.587 at 100%, 200% and 400% magnifications, respectively. Conclusion Based on the results, image magnification does not affect the accuracy of linear measurements made on CBCT scans. Interobserver reliability of pin length measurements was good at 200% magnification, while it was below the acceptable range at other magnifications. For measurement of pin diameters, this index was below the acceptable range at all magnifications.