This paper presents a comparison study of the experimental results from the falling weight deflectometer (FWD) test and laboratory resilient modulus test on granular subgrade materials and its application in flexible pavement design. Field and laboratory testing programs were conducted to develop a practical methodology for estimating resilient modulus (Mr) values of subgrade soils for use in the design of pavement structures. Soil characterization database was established for lab testing. A multiple regression model can be used to predict Mr value using several factors including soil properties, soil type and state of stresses for three popular American Association of State Highway and Transportation Officials (AASHTO) soil types (A-4, A-6, and A-7-6) in Indiana, and these prediction models developed were verified compared with laboratory Mr tests with high R2 value. In situ Mr seasonal variation based on abundant FWD test data in five field testing sites spread in Indiana was conducted in order to find the correlation between resilient modulus, temperature, and precipitation for the period from 2006 to 2012. The proposed method can accurately predict subgrade Mr of lab testing. However results from lab testing are significantly lower than recommended range by mechanistic-empirical pavement design guide (MEPDG) and backcalculation one using an adjust factor of 3. The design examples showed that the seasonal variation of temperature and precipitation as well as traffic can affect the design thickness by as much as 15 to 20 % in general. The findings of this study are expected to be helpful in the implementation of the pavement design in Indiana and elsewhere.