This study focuses on public exposure to natural radioactivity caused by the inhalation of radon and thoron progeny in homes in Franceville, Moanda and Mounana in Gabon. The equilibrium factor (FTn) between thoron and its progeny was determined experimentally for a proper estimate of the effective dose. In order to assess internal exposure due to radon and thoron progeny, 150 passive radon-thoron discriminative detectors (RADUET) and thoron progeny monitors were deployed for about 3 months in the above-mentioned towns. The results of the measurements obtained showed that the average concentrations of thoron progeny (EETC) were 1.54 ± 0.08 Bq m−3, 3.05 ± 0.09 Bq m−3 and 1.84 ± 0.11 Bq m−3 in Franceville, Moanda and Mounana, respectively. The ranges of the measured thoron equilibrium factors were 0.004–0.710, 0.005–0.750, and 0.006–0.794 in Franceville, Moanda and Mounana, respectively. The arithmetic and geometric mean values were, respectively, 0.183 and 0.117 in Franceville, 0.184 and 0.122 in Moanda, and 0.221 and 0.140 in Mounana. The experimentally determined equilibrium factor (FTnexp) allowed us to compare the value of the experimentally determined effective dose with the theoretically determined one calculated using the equilibrium factor proposed by United Nation Scientific Committee on the Effects of Atomic Radiation (UNSCEAR) 2000 report. FTnexp values were around 6–11 times greater than the UNSCEAR typical value. The ranges, arithmetic and geometric mean EERC values determined were 30.40–55.60 Bq m−3, 24.00 ± 0.90 Bq m−3 and 41.68 (1.00) in Franceville, 36.40–62.50 Bq m−3, 45.30 ± 0.70 Bq m−3 and 44.72 (1.00) in Moanda, and 35.00–90.00 Bq m−3, 50.00 ± 2.00 Bq m−3 and 48.50 (1.00) in Mounana. The mean values of the annual effective inhalation dose due to thoron progeny determined using FTnexp were 0.32 mSv (compared to 0.049 mSv), 0.63 mSv (compared to 0.103 mSv), and 0.39 mSv (compared to 0.055 mSv) in Franceville, Moanda and Mounana, respectively. The main conclusion of this study is that indirect estimations of thoron progeny concentrations considerably underestimate the estimation of the annual effective inhalation dose.