The encounter between Muslims and Japan coincides with the end of the 19th century. Japan, whom has closed itself to most of the world for about 250 years during the Tokugawa period, opened its doors to the world with the influence of the United States in 1853 and started to establish communication with many countries of the world. Following this, the encounters with Muslims and Islamic world also started. The first Muslims that arrived in Japan are thought to be merchants who came with the commerce ships. Thus, the journey of Muslims to Japan began with Indian Muslim merchants towards the end of the 19th century. Turko-Tatar Muslims who took shelter in Japan following the Russo-Japanese war in 1905 comes as the second significant Muslim immigrant group in Japan. During and after the Second World War the immigration slows down and the Indian and Turko-Tatar Muslims either returns to their homelands or immigrate other third countries. In the years following the war, although there were some individual visits, no significant migration activity from the Muslim countries is occurred. The third immigration wave coincides with the bubble economy of Japan after the 1970's. Many who sought better work conditions and salaries from countries such as Indonesia, Pakistan, Bangladesh and Iran found themselves in Japan. The current the number of Muslims in Japan, including short time migrants who came to work or study, residents who had already settled in the country, had families and started to raise second generations, and Japanese Muslims, is around 150,000.1 %10 of this number is considered as Japanese Muslims and the rest as immigrants. In the contemporary Japanese society, immigrant Muslims have a life away from discrimination, and do not have significant problems on fulfilling their religious needs with increasing number of mosques, masjids, Islamic organisations and halal food services. On the other hand, they still do not feel that they are being accepted as local members of the society. The aim of this study is to describe the Muslim migration history in Japan, and to analyse the current situation of migrants in Japan. In order to do this, the literature and the field study data derived in between 2016 September-2017 December and 2019 February-2010 January will be consulted. In this paper, we tried to explain that although the Muslim migration history to Japan has started more than a century ago, immigrant Muslims are still having hardships on being accepted as permanent part of the Japanese society. This could be of two reason. Firstly, due to unstable migration waves, and immigrants returning to their homelands or migrating to other countries, there was not a stable Muslim population in Japan until 80's. Although first mosques and education centers were established a long time ago, the number of Muslims in Japan has only started to increase after the migration wave of 70s. Secondly, Japanese has a habit of seeing foreigners as guests, on the grounds that foreigners cannot learn Japanese sufficiently and cannot adapt to Japanese customs, hence can never live like a Japanese. Because of these reasons, immigrant Muslims still have difficulty of feeling a belonging to the country they are residing in. However, the more they live in the country and the more they become proficient in the language, the more their life satisfaction increases, and they start to have meaningful relationships with the locals. [ABSTRACT FROM AUTHOR]