The work was carried out under the State Contract No. 114202010211 dated 17.08.2020, concluded between the Ministry of Transport of the Russian Federation and NIIAT JSC. The result is a methodology for assessing the socio-economic efficiency of transport operation in cities and urban agglomerations. In the process of performing the work the analysis of formation of the effects of transport functioning in cities and urban agglomerations was carried out, they were defined, classification was proposed, composition was established, methodological approaches to the cost estimate (monetization) of direct and indirect socio-economic effects, the effects of investment demand were developed and justified. The sequence of actions in the performance of efficiency assessment is defined, integral assessment indicators and formulas for their calculation are described. A list of indicators needed to conduct the assessment according to the methodology, indicating the source of information and reference to the regulatory document. When developing the methodology, the requirements of regulatory legal documents in the field of transport planning and organization of road traffic, as well as standards of transport services for the population were taken into account. The methodology is recommended for use in monitoring the current state of territorial transport systems, forecasting their development, as well as for the development of management decisions when implementing state transport policy.