We aimed to compare differences in performance and pacing variability indices between 5000 m heats and finals during major championships in men and women. Data with 100 m time resolution were used to compare overall pacing variability (standard deviation of 100 m section times, SD; and coefficient of variation, CV%) and short-term pacing variability (root mean square of successive differences between 100 m section times, RMSSD). The changes in performance and pacing indices differed between races and competitions. For instance, the men’s final in Beijing 2008 was quicker than the heat (p< 0.01) while the CV% was reduced (p= 0.03) and RMSSD increased (p< 0.01). For women, the heats and the final exhibited a similar mean time in London 2017 (p= 0.33) but with CV% (p< 0.001) and RMSSD (p< 0.001) showing opposite trends. Individual analyses of men’s and women’s champions revealed highly individual variability metrics. The use of RMSSD can complement overall variability indices for better characterization of pacing stochasticity.