Extreme temperatures impose thermal stress on human health, resulting in increased hospitalizations and mortality rate. We investigated the circulatory and respiratory causes of death for the years 2007 to 2014 inclusive for the urban and rural areas of Nicosia, Cyprus under urban heatwave and non-heatwave conditions. Heatwaves were defined as four or more consecutive days with mean urban daily temperature over the 90th percentile threshold temperature of the eight investigated years. Lag period of adverse health effects was found to be up to three days following the occurrence of high temperatures. The relative risk (RR) for mortality rate under heatwave and non-heatwave conditions was found taking in consideration the lag period. The results showed the increase of mortality risk particularly for men of ages 65–69 (RR = 2.38) and women of ages 65–74 (around RR = 2.54) in the urban area, showing that women were more vulnerable to heat extremities. High temperatures were also associated with high ozone concentrations, but they did not impose an excess risk factor, as they did not reach extreme values. This analysis highlights the importance of preparing for potential heat related health impacts even in Cyprus, which is an island with frequent heatwaves.