While there has been a tremendous decline in malaria disease burden in the remote parts of the Malaysia, little is known about malaria incidence in its urban localities. This study aimed to analyse trends of malaria cases in urban Kuala Lumpur, Malaysia. All suspected cases presented to a university hospital in Kuala Lumpur from January 2005 to December 2020 were examined by microscopy. Infection status was analysed using descriptive statistics and curve estimation analysis. Of 3105 blood films examined, 92 (3%) were microscopically confirmed malaria cases. Plasmodium vivax infections accounted for the majority (36.9%) of all malaria cases. Nearly half (47.8%) of cases were found among foreign cases (P<0.001). The majority of foreign cases were males (86.4%) and came from Southeast Asian countries (65.9%). Curve estimation analysis showed significant decreases of malaria cases due to P. vivax (R2 = 0.598; P<0.001) and Plasmodium falciparum (R2 = 0.0259, P = 0.029), but increase for Plasmodium knowlesi (R2 = 0.325, P = 0.021) during the 16 years. This study revealed that malaria incidence in urban Kuala Lumpur is low and has remained stable since 2005. However, P. knowlesi played a significant role in the increase of overall malaria in the area, highlighting the importance of continued vigilance and improved surveillance.