Panama disease, caused by the fungus Fusarium oxysporum f.sp. cubense (Foc), is one of the most important and destructive diseases in banana crops worldwide. There has been numerous studies into the infection process of this soil-borne pathogen, however, the extent of research into the movement of the pathogen through the rhizome and into the rest of the plant is limited. Furthermore, little is known about the lifecycle of the pathogen once it reaches the aerial components of the plant. In controlled PC2 glasshouse conditions, Cavendish ‘Williams’ (Musa AAA) and Lady Finger (Musa AAB) banana plants were inoculated using Foc Sub-tropical Race 4 (Foc STR4), which had been genetically transformed with a Green Fluorescent Protein (GFP). Every 10 days for 80 days, the plants were destructively harvested and examined using confocal laser microscopy to visualise the GFP Foc. All areas of the plant were examined, from the midrib of the leaves above the throat, through to the root tips. The results of this study show that the pathogen infects the plant through the roots and moves through the outer leaf sheaths of the pseudostem prior to external symptoms being presented. The movement of Foc was confined to both discoloured and healthy xylem vessels, and moved in an upward direction to the midrib in the apex of the leaf blade. Production of chlamydospores occurred within the air chambers of senescing leaf sheaths, while sporodochia formation and hyphal growth developed on the outside of senescing leaf sheaths. These result generate a greater understanding of the epidemiology of Foc, providing much needed knowledge to assist in the way infestations of Panama disease are managed in the future, as well as ongoing on-farm hygiene and biosecurity management.