Background Several vaccines have been approved for prevention of the coronavirus disease discovered on 31st December in Wuhan, China. Pakistan procured vaccines from various countries. However, the lack of knowledge and reluctance of the general population to embrace the use of the vaccines are considered to be the major determinants of the slow vaccination rate. Hence, it is necessary to evaluate the willingness of the general population about their perception of the COVID-19 vaccination. Methods A cross sectional survey based on a self-structured questionnaire comprising 18 questions was conducted (from April 21-June 21) on 400 Pakistani participants to evaluate their knowledge, attitude and perception towards the COVID-19 vaccination. Chi-square independent t-test and one-way Anova including a multiple step wise linear regression were used to draw conclusions about the results. P< 0.05 was considered significant. Results A total of 400 participants responded in the KAP survey of which 46.5% were female and 53.5% were male. The mean age of participants was 36.08 years. This survey showed a poor knowledge (50.5%), a fair attitude (75.1%) and a poor perception (58.1%) towards the COVID-19 vaccination. Higher mean knowledge and attitude scores was reported in the age group 21-40, females and unmarried urban citizens. Regression analysis showed that age, education, residence and employment status influenced the knowledge and perception score to a considerable extent. Conclusions The findings reflect an inadequate knowledge and perception on the one hand but a better attitude towards the COVID-19 vaccination. This KAP survey will help in better understanding the opinion of the general population towards vaccination and will be useful for policy makers and health care authorities aiming to increase the vaccination rate.