Giant molecular clouds (GMCs) are a new population of gamma-ray sources, being the target of cosmic rays (CRs) - locally accelerated or not. These clouds host very young stellar clusters where massive star formation takes place. Eventually, some of the stars are ejected from the clusters, becoming runaway stars. These stars move supersonically through the cloud and develop bowshocks where particles can be accelerated up to relativistic energies. As a result, the bowshocks present non-thermal emission, and inject relativistic protons in the cloud. These protons diffuse in theGMCinteracting with the matter.We present a model for the non-thermal radiation generated by protons and secondary pairs accelerated in the bowshocks of massive runaway stars within young GMCs. We solve the transport equation for primary protons and secondary pairs as the stars move through the cloud.We present non-thermal emissivity maps in radio and in gamma-rays as a function of time. We obtain X-ray luminosities of the order of ~1032 erg s-1 and gamma-ray luminosities ~1034 erg s-1. We conclude that, under some assumptions, relativistic protons from massive runaway stars interacting with matter in GMCs give rise to extended non-thermal sources.