We have accomplished deep tissue optical imaging of upconverting nanoparticles at 800 nm, using millisecond single pulse excitation with high peak power. This is achieved by carefully choosing the pulse parameters, derived from time-resolved rate-equation analysis, which result in higher intrinsic quantum yield that is utilized by upconverting nanoparticles for generating this near infrared upconversion emission. The pulsed excitation approach thus promises previously unreachable imaging depths and shorter data acquisition times compared with continuous wave excitation, while simultaneously keeping the possible thermal side-effects of the excitation light moderate. These key results facilitate means to break through the general shallow depth limit of upconverting-nanoparticle-based fluorescence techniques, necessary for a range of biomedical applications, including diffuse optical imaging, photodynamic therapy and remote activation of biomolecules in deep tissues.