Uncertain delay differential equations are a class of uncertain differential equations with time delay, which are widely used in population model, disease model, biological model, etc. How to estimate uncertain delay differential equations with unknown parameters is an important problem to be solved. Based on observed data, this paper uses least square estimation method to obtain estimated value of unknown parameters in the coefficients of uncertain delay differential equations. Numerical examples are introduced to show that least squares estimation method is suitable for uncertain delay differential equations. Application of uncertain SIS epidemic model with time delay further illustrates effectiveness of the method.