•Mass comparator for transporting and weighing sub-milligram weights presented.•Apparatus can handle weights such as wire weight, sheet weight, and disk weight.•Weighing tests of wire weights and sheet weights from 1 mg to 0.1 mg were performed.•Mass calibration of weight with nominal mass of 0.1 mg was realized. Sub-milligram mass standards are important to ensure the reliability of small mass measurements. A mass comparator capable of accurately transporting and weighing sub-milligram weights was developed at the National Metrology Institute of Japan. This apparatus can handle weights of various shapes such as wire weight, sheet weight, and disk weight. The weighing tests of wire weights and sheet weights ranging from 1 mg to 0.1 mg were performed using the developed apparatus. The mass calibration of weight with a nominal mass of 0.1 mg was realized with a standard uncertainty of 0.075 μg by comparing the test weight and the reference weight. This paper describes the details of the developed mass comparator, the standard deviation of the weighing value of the weight obtained using this apparatus, and the uncertainty of mass calibration of sub-milligram weights.