Gravitational lensing magnification is measured with a significance of 9.7 sigma on a large sample of galaxy clusters in the Canada-France-Hawaii Telescope Lensing Survey (CFHTLenS). This survey covers ~154 deg^2 and contains over 18,000 cluster candidates at redshifts 0.2 <= z <= 0.9, detected using the 3D-Matched Filter cluster-finder of Milkeraitis et al. (2010). We fit composite-NFW models to the ensemble, accounting for cluster miscentering, source-lens redshift overlap, as well as nearby structure (the 2-halo term), and recover mass estimates of the cluster dark matter halos in range of ~10^13 M_sun to 2*10^14 M_sun. Cluster richness is measured for the entire sample, and we bin the clusters according to both richness and redshift. A mass-richness relation M_200 = M_0 (N_200 / 20)^beta is fit to the measurements. For two different cluster miscentering models we find consistent results for the normalization and slope, M_0 = (2.3 +/- 0.2)*10^13 M_sun, beta = 1.4 +/- 0.1 and M_0 = (2.2 +/- 0.2)*10^13 M_sun, beta = 1.5 +/- 0.1. We find that accounting for the full redshift distribution of lenses and sources is important, since any overlap can have an impact on mass estimates inferred from flux magnification.