The need for protection and the attraction of opportunity continue to drive international migration, which has become one of the most sensitive policy issues. This human movement in search of better opportunities in the developed European countries has been predominantly called transit migration. Whether someone migrates to escape war, famine, persecution, natural catastrophes, economic depression, or just to find a chance for a better life, that person may find insecurity, human rights violations, and often destitution of their situation in the country of transit or destination. The degree to which human rights are violated, migrants are excluded from legal protection or redress and social work responses are provided effectively, varies widely among countries. The Republic of Macedonia has been among the European countries forced to develop specific responses to the unforeseen large-scale transit migration that affected the country during 2015–2016. Located directly on the transit route of Middle East refugees, the Republic of Macedonia found coping with the issue a huge challenge that resulted in periodic ill-treatment and human rights’ violations of migrants, accompanied with scarce social work activities which mostly served to mitigate the impact of human rights’ violations. The article initially presents a brief overview of international migration trends and instruments for protection of the human rights of migrants in general, as well as definitions and trends related to transit migration, in particular. Furthermore, with a purpose of highlighting the gaps between protection of migrants in paper (through international and domestic instruments) and in practice in the Republic of Macedonia, the article focuses on challenges and problems encountered regarding protection of human rights of transit migrants and social work support provided to them, in light of the recent 2015–2016 transit migration crisis.