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BACKGROUND: The spread and severity of the COVID-19 pandemic have been to such an extent that to shape an effective, collective response, governments need the participation of society and the cooperation of a wide range of civil society organizations and institutions. The objective of this study was to identify the activities of non-governmental organizations (NGOs) in response to the covid-19 pandemic in Iran and the challenges they confronted. METHODS: We conducted a qualitative analysis based on twenty-two individual, virtual, and semi-structured interviews. Interviewees were selected through purposeful and snowball sampling. All interviews were performed with active health-related NGO representatives willing to participate in the study and continued until data saturation. Data analysis was performed using qualitative content analysis. RESULTS: The activities and challenges raised by NGO representatives were identified in 6 main categories, including the need for the participation of NGOs in the fight against pandemics, response to the COVID-19 crisis in the society, challenges in providing services to the target group in the COVID-19 crisis, NGOs challenges in interacting with governmental and non-governmental institutions, information sources used by NGOs in the COVID-19 crisis and strategies to support NGOs in their efforts. CONCLUSION: Considering the crucial challenges for their participation, such as the NGO access to the target groups, lack of communication network, and constructive interaction between government institutions and the NGOs, it is recommended to increase the capacity of these institutions and intervene to establish a constructive and long-term relationship with the government.