The study set out to investigate the relationship between motivation and the level of employee performance. The study had three objectives; to examine the motivation practices used in KCCA, to examine factors affecting employee performance in KCCA, and to establish the relationship between motivation and employee performance. The study used a case study strategy which is Kampala Capital City Authority and an explanatory research design. To achieve the set objectives the study used stratified random sampling in sample selection by grouping the employees according to management levels. There after simple random sampling was applied to select respondents. A sample of 196 respondents was selected which comprised employees of Kampala Capital City Authority. The study revealed that KCCA carries out motivation of its employees in many ways including; provision of fringe benefits, paying bonuses to good workers, giving a sense of responsibility, promotion of consistently good workers and treating the workers equally. However, the study also revealed that the council does not use motivation tools including; remuneration, training, involvement of employees in decision making, and rotation of employees. The study further revealed that motivation is the major factor that affects employee performance. The study showed a direct strong and positive relationship between employee motivation and the performance of KCCA staff which is evidenced by the Pearson correlation of (r= 0,823**), significance level =0.01. Conclusively, the researcher found out that motivation has a positive influence on employee productivity and that if the management of KCCA strengthens their motivation practices, employees would perform more excellently hence attaining organizational goals. The researcher recommends that the council should always carry out thorough study on the various motivational practices that can motivate the specific employees such that they can apply the right tools appealing to the employees since the council’s biggest challenge had been using particular motivational tools which would act as dissatisfies to some employees.