Our aim was to compare an SRM® torque analysis system with a strain gauge instrumented pedals system for right and left peak crank torque, crank angle of peak torque and power output. Seven competitive cyclists performed an incremental test to exhaustion on a stationary cycle ergometer equipped with an SRM® torque analysis system and a strain gauge instrumented pedals system (SGI pedals). The SRM® torque analysis system measured net torque while the SGI pedals measured the normal and anterior-posterior force applied on the pedal surface. Forces on the pedal surface were resolved into forces on the cranks (tangential and radial). Crank torque was measured by the pedals using the tangential force on the cranks and crank length. Power output was calculated from crank torque and angular velocity of the crank (calculated from pedalling cadence). All data were acquired between the 20th and the 40th seconds of each stage of the incremental test. Magnitudes of differences between outputs from the SGI pedals and the SRM® torque analysis system were assessed by effect sizes. Power output was higher for the SRM® torque analysis system than the SGI pedals. Peak torques were lower for the SRM® torque analysis system compared to the SGI pedals. The angle of the right and left peak torque increased for the SRM® torque analysis system compared to the SGI pedals. The SRM® torque analysis system overestimated power output, underestimated peak torque and increased the angle of peak torque compared to the SGI pedals. Where possible a strain gauge instrumented pedals system should be used to measure performance variables of cyclists rather than the SRM® torque analysis system.