Equatorial warming conditions in urban areas can influence the particle number concentrations (PNCs), but studies assessing such factors are limited. The aim of this study was to evaluate the level of size-resolved PNCs, their potential deposition rate in the human respiratory system, and probable local and transboundary inputs of PNCs in Kuala Lumpur. Particle size distributions of a 0.34 to 9.02 μm optical-equivalent size range were monitored at a frequency of 60 s between December 2016 and January 2017 using an optical-based compact scanning mobility particle sizer (SMPS). Diurnal and correlation analysis showed that traffic emissions and meteorological confounding factors were potential driving factors for changes in the PNCs (Dp ≤1 μm) at the modeling site. Trajectory modeling showed that a PNC <100/cm3 was influenced mainly by Indo-China region air masses. On the other hand, a PNC >100/cm3 was influenced by air masses originating from the Indian Ocean and Indochina regions. Receptor models extracted five potential sources of PNCs: industrial emissions, transportation, aged traffic emissions, miscellaneous sources, and a source of secondary origin coupled with meteorological factors. A respiratory deposition model for male and female receptors predicted that the deposition flux of PM1 (particle mass ≤1 μm) into the alveolar (AL) region was higher (0.30 and 0.25 μg/h, respectively) than the upper airway (UA) (0.29 and 0.24 μg/h, respectively) and tracheobronchial (TB) regions (0.02 μg/h for each). However, the PM2.5 deposition flux was higher in the UA (2.02 and 1.68 μg/h, respectively) than in the TB (0.18 and 0.15 μg/h, respectively) and the AL regions (1.09 and 0.91 μg/h, respectively); a similar pattern was also observed for PM10.