Sperm competition is a post-copulatory sexual selection mechanism in species in which females mate with multiple males. Despite its evolutionary relevance in shaping male traits, the genetic mechanisms underlying sperm competition are poorly understood. A recently originated multigene family specific to D. melanogaster, Sdic, is important for the outcome of sperm competition in doubly-mated females, although the mechanistic nature of this phenotype remained unresolved. Here we compared doubly-mated females, second mated to either Sdic knockout or non-knockout males, and directly visualize sperm dynamics in the female reproductive tract. We found that a less effective removal of first-to-mate male’s sperm within the female’s sperm storage organs is consistent with a reduced sperm competitive ability of the Sdic knockout males. Our results highlight the role young genes can play in driving the evolution of sperm competition.