We use mobile phone usage data to measure the extent of segregation of Syrian refugees in Turkey, and analyze its role in their internal mobility patterns. We construct a range of dissimilarity and normalized isolation indices using the hourly phone call volume of refugees and natives. The richness of the data allows us to compute the indices across different provinces and over time. Segregation levels show high variation across the country, with significantly lower levels of segregation in provinces with a higher share of refugees. Refugee mobility across provinces over time appears to be negatively correlated with segregation at destination, while native mobility is not. Based on data from Istanbul, segregation does not influence intra-province mobility. This is possibly due to the differences in segregation indices across the hours of the day, suggesting that residential segregation is higher than labor market segregation.