The goal of section speed control is to increase speed limit compliance in the monitored road sections, decrease speed variance and improve traffic safety. General experience with section speed control on motorways is positive, with significant improvements in both speed and safety performance. The presented study focused on a unique application of section speed control in motorway work zones in the Czech Republic. Effectiveness was monitored (in terms of average speed, speeding and accident rates) in three sections and four time periods (normal operation, work zone, work zone with section speed control, normal operation), which allowed discerning individual effects of work zone and section speed control. In addition, a novel data source—floating car data—was used. Work zones were found to increase accident rates compared to normal operation and decrease with the introduction of section speed control. The effects on average speed, speed variance and speeding were positive, although smaller compared to the studies conducted in non-work zone conditions.