The coronavirus impacted various sectors and economies around the globe in a very drastic way because of its limited manpower, materials, and machines, and the construction sector is not an exemption. As the industry is the most prominently dependent on labor and material, they have experienced an adverse effect on their economy, causing delays in the schedule and ultimately leading to cost overruns. Although many studies have been conducted to understand the causes of the cost overruns among different sectors during COVID-19, no study analyzed the factors affecting cost based on the size and type of construction sector. Therefore, this study aims to identify various challenges the construction industry faced during the pandemic and analyze the identified challenges affecting project cost based on the size and type of construction sector. A comprehensive literature search was performed, followed by developing and distributing a questionnaire survey. Sixty-two responses were received and were analyzed based on the size and type of the organization. The study's results revealed that cost overruns due to escalating and inflation of material prices and increased demand from suppliers and manufacturers were identified as the most critical challenges that affected the project cost during the pandemic. Interestingly, it was found that an organization's size and type play a vital role in how it is affected. The results of this study will assist researchers and professionals in the industry in developing preventive measures to manage cost overruns based on the size and type of an organization during any similar pandemics in the future.