This study characterized COVID-19 transmission in Ghana in 2020 and 2021 by estimating the time-varying reproduction number (Rt) and exploring its association with various public health interventions at the national and regional levels. Ghana experienced four pandemic waves, with epidemic peaks in July 2020 and January, August, and December 2021. The epidemic peak was the highest nationwide in December 2021 with Rt ≥ 2. Throughout 2020 and 2021, per-capita cumulative case count by region increased with population size. Mobility data suggested a negative correlation between Rt and staying home during the first 90 days of the pandemic. The relaxation of movement restrictions and religious gatherings was not associated with increased Rt in the regions with fewer case burdens. Rt decreased from > 1 when schools reopened in January 2021 to < 1 after vaccination rollout in March 2021. Findings indicated most public health interventions were associated with Rt reduction at the national and regional levels.