Epoxy resins are extensively used in the fabrication of fibre reinforced polymer (FRP) composites as well as in adhesive compounds. However, the brittleness of cured epoxy resins results in low resistance against crack formation and propagation. A practical approach to address the brittleness of epoxies is by incorporating additives in their structure [1, 2]. In the present study, two different inclusions, (i) functionalised carbon nanotubes (CNTs, nanoscale) and (ii) a phase-separating thermoplastic (TP, microscale), polyetherimide (PEI), were simultaneously incorporated into an epoxy (diglycidyl ether of bisphenol A) to assess their influence on fracture toughness. Two different methods for introducing the CNTs were investigated to manufacture the ternary nanocomposite: adding CNTs to the neat epoxy (method I) and adding CNTs to the thermoplastic component (method II). It was found out that, in both methods, the addition of CNTs had a significant impact on the distribution of the thermoplastic in the matrix without changing the degree of phase separation. Moreover, microscopic imaging revealed that CNTs had a better dispersion in the ternary nanocomposite made by method I. The bridging of thermoplastic and the pull-out of CNTs are regarded as the primary energy dissipating mechanisms of the ternary nanocomposite. A good dispersion and a higher degree of TP phase deformation in the nanocomposite, prepared by method I, led to a higher fracture toughness. Hence it is suggested that mixing CNTs with the neat epoxy prior to the addition of thermoplastic toughening additives is a more effective way to improve the properties of nanocomposite.