This study proposed a framework of the Pioneer 3-AT (P3-AT) autonomous robot for pavement inspection that was integrated with a highly accurate virtual reference station (VRS) positioning technique. The two test sites were 60 km apart; one was rigid pavement and the other was flexible pavement. Two VRS systems were adopted: (1) A VRS system developed by Taiwan Control Signal Co., Limited and (2) Virtual Base Station Real-Time Kinematic (also called e-GPS system) from Taiwan National Land Surveying and Mapping Center. First, the tire pressure and horizontal movement of the P3-AT were calibrated on the two test sites. Then the accuracy of the positioning data provided by VRS to guide the P3-AT was investigated under both static and dynamic conditions at distances of movement from 0.25 to 20 m, to verify the stability and feasibility of this framework. We observed that standard deviations in positioning were less than 0.03 m and rms values were close to prescribed distances in static tests. The reproducible errors were less than 0.03 m in dynamic tests. The results showed that the two VRS systems were able to provide the P3-AT with accurate positioning data on the two test sites. This study also successfully demonstrated the use of the P3-AT in autonomously surveying surface distresses and manholes and its ability to accurately plot slabs on a rigid pavement. Since the P3-AT possesses the properties of low volume, slow speed, flexible modules, and low price, this study confirms that the P3-AT integrated with the VRS positioning technique has the potential to provide significant assistance in automatic pavement inspections of specific areas, such as airports, and for particular purposes, such as Quality Control/Quality Assurance testing.