This study is focused on the regional variation of rainfall (RF) in Pakistan using wavelet transformation. The RF variation in five regions of Pakistan, namely, Karachi, Lahore, Peshawar, Quetta and Islamabad are investigated. The highest variability was observed from 1961 to 2015 in a monthly data set for each region. The results reveal that the main variation is observed in the middle phase of each RF signal and some in the recovery phase (initial and end) using Daubechies (db 2) wavelet. In addition, the study reveals that the maximum RF variability occurred in 1–4-year periodicity using the Morlet wavelet. This caused moisture and led to more RF received in cities. Karchi, Peshawar, and Quetta show a decrease in RF as compared to Lahore and Islamabad. We also estimated the role of significant ENSO periodicity for 8–16 years in increasing RF observed post-1970 and pre-1970, and after 2000, showing neutral or decreasing RF. Finally, based on these results, Islamabad and Lahore are the wettest cities observed as compared to Karachi, Peshawer and Quetta, which represent the drier cities with low RF.