The nano-scale spin torque oscillator (STO) is a compelling device for on-chip, highly tunable microwave frequency signal generation. Currently, one of the most important challenges for the STO is to increase its longer-time frequency stability by decreasing the 1/f frequency noise, but its high level makes even its measurement impossible using the phase noise mode of spectrum analyzers. Here, we present a custom made time-domain measurement system with 150 MHz measurement bandwidth making possible the investigation of the variation of the 1/f as well as the white frequency noise in a STO over a large set of operating points covering 18–25 GHz. The 1/f level is found to be highly dependent on the oscillation amplitude-frequency non-linearity and the vicinity of unexcited oscillation modes. These findings elucidate the need for a quantitative theoretical treatment of the low-frequency, colored frequency noise in STOs. Based on the results, we suggest that the 1/f frequency noise possibly can be decreased by improving the microstructural quality of the metallic thin films.