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Background Nigeria’s population is projected to increase from 200 million in 2019 to 450 million in 2050 if the fertility level remains at the current level. Thus, we examined the shifts in the age pattern of fertility, timing of childbearing and trend in fertility levels from 2003 and 2018 across six regions of Nigeria. Method This study utilised the 2003, 2008, 2013, and 2018 Nigeria Demographic and Health Survey datasets. Each survey was a cross-sectional population-based design, and a two-stage cluster sampling technique was used to select women aged 15–49 years. The changes in the timing of childbearing were examined by calculating the corresponding mean ages at the birth of different birth orders for each birth order separately to adjust the Quantum effect for births. The Gompertz Relational Model was used to examine the age pattern of fertility and refined fertility level. Result In Nigeria, it was observed that there was a minimal decline in mean children ever born (CEB) between 2003 and 2018 across all maternal age groups except aged 20–24 years. The pattern of mean CEB by the age of mothers was the same across the Nigeria regions except in North West. Nigeria’s mean number of CEB to women aged 40–49 in 2003, 2008, 2013 and 2018 surveys was 6.7, 6.6, 6.3 and 6.1, respectively. The mean age (years) at first birth marginally increased from 21.3 in 2003 to 22.5 in 2018. In 2003, the mean age at first birth was highest in South East (24.3) and lowest in North East (19.4); while South West had the highest (24.4) and both North East and North West had the lowest (20.2) in 2018. Similar age patterns of fertility existed between 2003 and 2018 across the regions. Nigeria’s estimated total fertility level for 2003, 2008, 2013 and 2018 was 6.1, 6.1, 5.9 and 5.7, respectively. Conclusion The findings showed a reducing but slow fertility declines in Nigeria. The decline varied substantially across the regions. For a downward change in the level of fertility, policies that will constrict the spread of fertility distribution across the region in Nigeria must urgently be put in place.