The use of gold nanorods (GNRs) as a contrast agent in bioimaging and cell tracking has numerous advantages, primarily due to the unique optical properties of gold nanorods which allow for the use of infrared regions when imaging. Owing to their unique geometry, Au NRs exhibit surface plasmon modes in the near-infrared wavelength range, which is ideal for carrying out optical measurements in biological fluids and tissue. Gold nanorod functionalization is essential, since the Cetyltrimethyl ammonium bromide CTAB gold nanorods are toxic, and for further in vitro and in vivo experiments the nanorods should be functionalized to become optically stable and biocompatible. In the present study, gold nanorods with an longitudinal surface plasmon resonance (LSPR) position around 800 nm were synthesized in order to be used for photoacoustic imaging applications for stem cell tracking. The gold nanorods were functionalized using both thiolated poly (ethylene glycol) (PEG) to stabilize the gold nanorods surface and a CALNN-TAT peptide sequence. Both ligands were attached to the gold nanorods through an Au-sulfur bond. CALNN-TAT is known as a cell penetrating peptide which ensures endocytosis of the gold nanorods inside the mesenchymal stem cells of mice (MSCD1). Surface modifications of gold nanorods were achieved using optical spectroscopy (UV-VIS), electron microscopy (TEM), zeta-potential, and FTIR. Gold nanorods were incubated in MSCD1 in order to achieve a cellular uptake that was characterized by a transmission electron microscope (TEM). For photoacoustic imaging, Multi-Spectral Optoacoustic Tomography (MSOT) was used. The results demonstrated good cellular uptake for PEG-CALNN-TAT GNRs and the successful use of modified gold nanorods as both a contrast agent in photoacoustic imaging and as a novel tracking bioimaging technique.