This paper presents a novel thickness profile measuring system that measures double-sided thin pipe wall surfaces in a non-contact, continuous, cosine error-free, and fast manner. The surface metrology tool path was developed to align the displacement sensors always normal to the double-sided surfaces to remove cosine error. A pair of capacitive type sensors that were placed on the rotary and linear axes simultaneously scans the inner and outer surfaces of thin walls. Because the rotational error of the rotary axis can severely affect accuracy in thickness profile measurement, such error was initially characterized by a reversal method. It was compensated for along the rotational direction while measuring the measurement target. Two measurement targets (circular and elliptical metal pipe-type thin walls) were prepared to validate the developed measurement method and system. Not only inner and outer surface profiles but also thin wall thickness profiles were measured simultaneously. Based on the output data, the circularity and wall thickness variation were calculated. The thickness profile results showed good agreement with those obtained by a contact type micrometer (1 µm resolution) at every 6 degrees interval. The uncertainty budget for this measuring system with metrology tool path planning was estimated at approximately 1.4 µm.