Modification of bone is continuous throughout life and influenced by many factors, including physical activity. This study investigated changes in areal bone mineral density (aBMD) and hip structure among male and female collegiate distance runners and non-athlete controls over 12 months. Using dual-energy x-ray absorptiometry (DXA) and hip structure analysis (HSA) software, aBMD at the posterior-anterior (PA) and lateral spine, femoral neck, total hip (TH), whole body (WB), and bone geometry at the narrow neck (NN) of the femur was measured three times over 12 months. HSA included cross-sectional area (CSA), cross-sectional moment of inertia (CSMI), and Z-section modulus (Z). Male runners had significantly higher aBMD at TH and WB and greater CSA, CSMI, and Z than male controls at the end of 12 months. Female controls had higher aBMD at the PA spine than female runners at the end of 12 months. Male runners had significant increases in aBMD at the PA ( = 0.003) and lateral spine ( = 0.002), and TH ( = 0.002), female runners had significant decreases in aBMD at TH ( = 0.015) and WB (p = 0.002), male controls had significant increases in aBMD at the PA spine ( < 0.001) and WB (p < 0.001), and female controls had significant decreases in aBMD at lateral spine and TH ( = 0.008) over the year. When applying covariates of bone-free lean mass and vitamin D, male distance runners demonstrated significant improvement in CSA (3.602 ± 0.139 vs. 3.675 ± 0.122 cm,  = 0.05), CSMI (3.324 ± 0.200 to 3.467 ± 0.212 cm,  < 0.05), and Z (1.81 ± 0.08 to 1.87 ± 0.08 cm, p = 0.05) during the study. No other changes in hip structure occurred over the year. Distance running may be beneficial to aBMD and hip structure in college-age males but not females. Further research is needed on potential influences of weight-bearing activity, energy availability, and hormonal status on aBMD and hip structure in males and females.