Creating new construction materials with improved strength, elasticity, and durability properties represent the focus of many research works. Significant research effort has been invested in investigating the use of carbon nanotubes (CNTs) in cementitious materials, especially multi-walled carbon nanotubes (MWCNTs) which consist of a series of concentric graphite tubes. The use of MWCNTs is closely related to the use of surfactants and ultra-sonication procedures which may alter their properties and the properties of cement-based materials. The paper presents the preliminary results of an experimental investigation on the suitability of using a new, modified, MWCNT type aimed at eliminating the need of using surfactants and ultrasonication. The modified MWCNTs have a much lower surface energy compared to “classical” ones which would result in a decreased tendency of self-aggregation. A comparison was carried out from the point of view of density, flexural and compressive strength as well as dynamic modulus of elasticity of the obtained mortars. The mortar mix incorporating the modified MWCNTs showed improved mechanical properties even for a low percentage of CNT addition (0.025% by mass of cement). The results are discussed based on the material structure determined from a series of scanning electron microscopy (SEM) and X-ray diffraction (XRD) analyses.