We report on the structural stability of ideal (defect-free) and structurally and morphologically degenerate carbon nanotubes and nanotube junction systems under axial loading based on the finite element method. We estimated the values for critical buckling load for uncapped and capped single-walled carbon nanotubes (SWCNTs) and linear and angle-adjoined SWCNT heterojunctions in ideal and structurally degenerate systems containing single-, double-, triple-, pinhole- and pentagon–heptagon (i.e., 5–7) structural defects and also containing a substitutional nitrogen (N) atom inclusion under compressive loading. Absolute atomic vacancy (defect) concentration in studied SWCNTs models was assumed to be nil for ideal systems, and was up to 3.0 at.% for structurally and morphologically degenerate systems. It was found that all types of structural defects and the morphological N-defect had reduced the load carrying capacity and mechanical strength in all SWCNT systems studied. The SWCNT models containing physically large vacant sites, such as triple- and pinhole-defects, displayed significantly lower critical load values compared to the systems that contained only a single-, double- or triple-vacancies. In addition, we found that capped SWCNTs performed marginally better in critical load carrying capacity compared to uncapped SWCNT systems. Furthermore, majority of the investigated structures displayed reduced load in SWCNTs with narrower tube widths, proportional to the size and the type of the defect investigated. The effects of chirality, such as zigzag- versus armchair-type, on the structural stability of the investigated SWCNT models were also investigated.