In this study, a realistic model for dynamic instability of embedded single-walled nanotubes (SWCNTs) conveying pulsating fluid is presented considering the viscoelastic property of the nanotubes using Kelvin–Voigt model. SWCNTs are placed in longitudinal magnetic fields and modeled by sinusoidal shear deformation beam theory (SSDBT) as well as modified couple stress theory. The effect of slip boundary condition and small size effect of nano flow are considered using Knudsen number. The Gurtin–Murdoch elasticity theory is applied for incorporation the surface stress effects. The surrounding elastic medium is described by a visco-Pasternak foundation model, which accounts for normal, transverse shear and damping loads. The motion equations are derived based on the Hamilton's principle. The differential quadrature method (DQM) in conjunction with Bolotin method is used in order to calculate the dynamic instability region (DIR) of visco-SWCNTs induced by pulsating fluid. The detailed parametric study is conducted, focusing on the combined effects of the nonlocal parameter, magnetic field, visco-Pasternak foundation, Knudsen number, surface stress and fluid velocity on the dynamic instability of SWCNTs. The results depict that increasing magnetic field and considering surface effect shift DIR to right. The results presented in this paper would be helpful in design and manufacturing of nano/micro mechanical systems.