Cloud computing can help organizations accomplish more by paying less and breaking the physical boundaries between IT infrastructure and its users, however heightened security threats must be overcome in order to benefit fully from this new computing exemplar. The objective of this research was to determine the fundamental cloud security challenges experienced by SMEs in Kenya. Descriptive survey was therefore chosen for this study because the researcher was interested in the opinions of the respondents in terms of security challenges in cloud computing. The primary area of study for this research was Nairobi, Kisumu and Mombasa and the target population for this study were the Top 100 SME companies in Kenya as of 2016. This information could be useful and vital to policy makers and researchers who are making efforts to improve security in the field of Cloud Computing.