The Nigerians were economic migrants stuck in Saudi Arabia after being caught up in the coronavirus restrictions and needed assistance returning home.
The repatriation came after one group made a video which circulated on social media showing them in squalid conditions and calling for help.
"Many of you travelled expecting to return at a particular time but COVID-19 came in, and during this period, movements were restricted and that is how many of you were stranded," aviation ministry official Bolaji Akinremi said.
"Many of you went in search of greener pasture - jobs and different experiences, you are back home with an opportunity to start another life."
The group of a total of 800 Nigerians will be flown back between Thursday and Friday. The first group of 384 included 83 women and one infant.
The returnees were transported to a camp for Covid-19 screening and testing after which they will be quarantined for 14 days before reuniting with their families, officials said.
The United Nations said late last year that more than 2.7 million migrants who wished to return home have been stranded abroad because of restrictions put in place to fight the coronavirus pandemic.
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