Background During the assembly and maintenance of cilia, precursor proteins need to be transported from the cell body into the organelle. Intraflagellar transport (IFT) is assumed to be the predominant protein transport pathway in cilia, but it remains largely unknown how ciliary proteins use IFT to reach their destination sites in the cilium and whether the amount of cargo transported by IFT is regulated. Results Single-particle imaging showed that DRC4, a structural protein of the axoneme, moves in association with IFT particles inside Chlamydomonas reinhardtii cilia. IFT is required for DRC4 transport both into and within the cilium. DRC4 cargoes dissociate from IFT trains at the tip as well as at various sites along the length of the cilium. Unloaded DRC4 diffuses before docking at its axonemal assembly site. In growing cilia, DRC4 transport by IFT was strongly increased over the steady-state level, and the frequency decreased linearly with the increasing ciliary length. The frequency of DRC4 transport was similarly elevated in short growth-arrested cilia and remained high even when the amount of DRC4 available in the cell body was reduced. Conclusions DRC4 is a bona fide cargo of IFT. Incompletely assembled cilia trigger an increase in the amount of DRC4 cargo transported by IFT particles, and DRC4 transport is downregulated as cilia approach their steady-state length. We propose a model in which ciliary length is controlled by regulating the amount of cargo transported by IFT particles.