The analysis of the relationship between the refugee influx in Kenya and insecurity from 1991 – 2016, brings out a different perception. The study in seeking to investigate the effects of refugee influx on security in Kenya, the contribution of refugees to proliferation of small arms in Kenya and to critically analyze the role of the Government of Kenya in handling refugee issues vs. security concerns separates refugee issues from security issues. The analysis of human security concept, translates to respect of human rights while handling refugees issues. The research focused on investigating the refugee situation in Kenya’s structure and strategies in the management of refugee affairs. The study looks deeper into the various linkages that the refugee situation presents in its management nationally and regionally. The study seeked to investigate the security issues caused by refugees and refugee are how refugees are connected to terrorism.