Zakat is a tool under the ijtimaie sector apart from waqf, sadaqah and infaq that can be used to share wealth among the Muslims. To a Muslim, paying zakat is equally important as paying tax as a good citizen since both produce positive impacts to the societies. In modern days, the zakat and taxation systems run in parallel in many countries with huge Muslims populations or even with low number of Muslims population. This practice can be seen in countries like Malaysia, Indonesia and Singapore. This practice poses the question, whether or not the Muslims are being burdened by double payment in the form of zakat and taxation. Despite the importance of zakat and taxation, many studies in zakat have not attempted to discover how zakat is being recognized in the tax systems. In view of the foregoing, this article discusses how zakat is being recognized in the taxation systems of Malaysia and Indonesia. The analysis indicates that both taxation systems in Malaysia and Indonesia recognize the importance of zakat. However, the treatment of zakat is different in Malaysia and Indonesia which produces different tax impact to the taxpayers who at the same time paying zakat. The findings are beneficial to the taxpayers in both countries in understanding the tax treatment of zakat in taxation especially if they are interested to generate income in Malaysia or Indonesia