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At high redshifts, protogalaxies were forming their first generations of stars in intense bursts. During their active phases, these starburst galaxies would presumably be environments rich in energetic cosmic rays due to the presence of massive stars and their remnants. Stellar remnants can supply seed particles and generate the shocks (via supernova explosions and other violent events) needed to accelerate the seeds to very high energies. I will present an overview of my current research activities, which consider the effects these energetic cosmic rays can have on the early Universe, particularly on the formation and evolution of the galaxies therein. I will outline how these energetic particles can interact with protogalactic environments, and discuss the impacts they may have on the evolution and star-formation histories of their hosts, how their astrophysical effects can manifest themselves on galactic, sub-galactic and super-galactic scales, and how their signatures might be observed in the CTA era.