This study was to establish the relationship between income tax administration and profitability of small-scale business enterprises in Kampala Capital City, Kampala district. The study aimed at assessing the profitability of business enterprises in Kampala Capital City; finding out if taxpayers are aware of all their tax obligations, know how income tax is administered, policies and problems affecting them as well as their businesses. The study was guided by the following research objectives; to establish how income tax administration is administered and imposed on small-scale business enterprises, to assess the profitability of small-scale business enterprises, to establish the relationship between income tax administration and profitability of small-scale business enterprises in Uganda. The study applied both qualitative and quantitative research designs where interviews and Questionnaires were used. Data was collected from both primary and secondary sources. Data was processed and analyzed using formal tables, pie charts, graphs, narrative text, and correlation to find out the relationship between income tax administration and profitability of small scale businesses. A total of 50 respondents were considered out of the entire population in the district. The findings revealed that income tax administration is poor and this was shown in the findings that indicated that the business community is not adequately sensitized, tax rates are at times high and they are based on estimates.