This study has two main purposes; first, it examines the effect of capital structure on profitability of Islamic and conventional banks; second, it determines that whether the capital structure of Islamic and conventional banks is same or not. A sample of ten banks was taken over the period 2006-2016. Independent samples T-test was used for finding the comparison between the capital structure of Islamic and conventional banks while for assessing the impact of capital structure on profitability, regression analysis (Fixed effects model) was used. Results showed that the capital structure of both types of banks was similar except for bank size which differed significantly. Moreover, ROA was negatively correlated to the capital structure of both conventional and Islamic banks. In contrast, ROE was positively correlated to the capital structure of both conventional and Islamic banks. In addition to that, two explanatory variables were positively correlated while two were negatively correlated to EPS for both Islamic and conventional banks. This study proves the existence of prominent theories of capital structure (pecking order theory and trade-off theory) for both conventional and Islamic banks in Pakistan and also validates the economies of scale.