GeCo2O4 is a unique system in the family of cobalt spinels ACo(2)O(4) (A= Sn, Ti, Ru, Mn, Al, Zn, Fe, etc.) in which magnetic Co ions stabilize on the pyrochlore lattice exhibiting a large degree of orbital frustration. Due to the complexity of the low-temperature antiferromagnetic (AFM) ordering and long-range magnetic exchange interactions, the lattice dynamics and magnetic structure of a GeCo2O4 spinel have remained puzzling. To address this issue, here we present theoretical and experimental investigations of the highly frustrated magnetic structure, and the infrared (IR) and Raman-active phonon modes in the spinel GeCo2O4 , which exhibits an AFM ordering below the Ned temperature T-N similar to 21 K and an associated cubic (Fd (3) over barm) to tetragonal (I4(1)/amd) structural phase transition whose location at TN vs at a lower T-s similar to 16 K is controversial. Our density functional theory (DFT+U) calculations reveal that one needs to consider magnetic-exchange interactions up to the third-nearest neighbors to get an accurate description of the low-temperature AFM order in GeCo2O4. At room temperature, three distinct IR-active modes (T-1u) are observed at frequencies 680, 413, and 325 cm(-1) along with four Raman-active modes A(1g), T-2g(1), T-2g(2), and E-g at frequencies 760, 647, 550, and 308 cm(-1), respectively, which match reasonably well with our DFT-PU calculated values. All the IR-active and Raman-active phonon modes exhibit signatures of moderate spin-phonon coupling. The temperature dependence of various parameters, such as the shift, width, and intensity, of the Raman-active modes is also discussed. Noticeable changes around T-N similar to 21 K and T-S similar to 16 K are observed in the Raman line parameters of the E-g and T-2g(1) modes, which are associated with the modulation of the Co-O bonds in CoO6 octahedra during the excitations of these modes.