Flooding can have an effect on each thing of our lives, including road transportation. This study investigated the causes and the effects of flooding on road transportation in Rwanda, Kigali city and contributed to the mitigation measures. The data were collected by administering 150 questionnaires on the respondents within the study area and by physical survey. The hypotheses were formulated and tested using the statistical method of student’s t- test and the data displayed a significant difference (P<0.05). The results of this study revealed that heavy rains, poor drainage systems, illegal disposal of waste in drains, and poor construction and maintenance of roads are the main causes of road flooding in the city of Kigali. The effects of floods on road transportation include traffic jam and increased travel time, damage to road structures, blockage of drains and traffic accidents in the study area. The study recommends green storm water infrastructure practices, good road construction works, controlled dumping sites, the construction and maintenance of drainage systems and an immediate government response to the threat of flooding to address the challenges of flooding on road transportation in the city of Kigali.