The University of Tasmania Ceduna radio telescope has been used to investigate rapid variability in the radio flux density of the BL Lac object PKS B1144−379 at 6.7 GHz. High-cadence monitoring of this extreme scintillator was carried out over a period of approximately 9 yr, between 2003 and 2011. We have used structure functions created from the intensity time-series to determine the characteristic time-scale of the variability. The characteristic time-scale is consistently observed to increase during certain periods of each year, demonstrating the annual cycle expected for scintillation through an interstellar scattering screen. The best-fitting annual cycle model for each year suggests that the scintillation pattern has an anisotropic structure and that the upper limit of its scattering screen is at a distance of ∼0.84 kpc. Higher anisotropy in some of the annual cycle fits suggests that changes in the intrinsic source structure might be influencing the variability time-scale. We found a prominent annual cycle is only present in the variability time-scale for certain years, where other evidence suggests that the core is compact. From our measurements, we calculated that the core angular size varied between 5.65 and 15.90 μas (0.05–0.13 pc). The core component was found to be at its most compact during two flares in the total flux density, which were observed in 2005 and 2008. We conclude that the long-term variability in the radio flux density of PKS B1144−379 is due to intrinsic changes in the source and that these affect our ability to measure an annual cycle in its variability time-scale.