Irrigated rice (Oryza sativa L.) is a crop of extreme social and economic importance in Brazil, and the state of Rio Grande do Sul accounts for >70% of the national production. The Brazilian Agricultural Research Corporation (Embrapa) is focused on rice breeding, with the aim of developing cultivars with significantly increased grain yield and improved sustainability. The objective of this study was to estimate the genetic progress of 45 yr of the irrigated rice breeding program of Embrapa in Southern Brazil from 1972 to 2016 by conducting a comparative analysis of cultivars in the same environment and by meta‐analysis of line yield assays. The estimates were results from a meta‐analysis obtained by evaluating 455 genotypes in 145 trials of regional line yield and value for cultivation and use of 44 agricultural crop seasons, and by comparing cultivars obtained by evaluating 25 cultivars in 10 agricultural crop seasons. Genetic gains were evaluated for grain yield, plant height, and days to flowering. The cultivars released by the breeding program were also evaluated for important agronomic characters. The genetic estimates determined a genetic progress for grain yield via meta‐analysis and via comparison of cultivars of 0.62 (37.91 kg yr−1) and 0.73% (47.78 kg yr−1), respectively. It was also verified that during the period there was a reduction in plant height and days to flowering. Three distinct historical phases that defined changes in research focus and in genetic gains can be described: (i) 1972 to 1983, before the rice Green Revolution; (ii) 1983 to 2000, after the rice Green Revolution; and (iii) 2000 to 2016, selection intensification for industrial grain quality attributes. Other relevant genetic aspects, selection strategies, and phases of the breeding program were discussed.