The Dutch side recovered from conceding an equaliser to dominate the second half after Midtjylland were reduced to 10 men, recording their second consecutive victory in the competition.
Ajax made a bright start and took the lead in the ninth minute when Arokodare headed home Oscar Gloukh’s corner.
The Nigerian had initially fired wide after Owen Wijndal’s cross was parried into his path, but he made no mistake with his next opportunity to give the visitors an early advantage.
Midtjylland responded in the 28th minute. Gue-Sung Cho flicked on a ball for Friday Etim, who showed excellent composure to get past Thilo Kehrer before rounding goalkeeper Marc ter Stegen and finishing into an empty net.
However, the hosts suffered a major setback shortly before half-time when Kjell Wätjen received a second yellow card in the 43rd minute for a foul on Abdellah Ouazane.
Ajax took advantage of their numerical superiority five minutes after the restart. Ouazane supplied the pass for Arokodare, who produced a brilliant finish to restore the visitors' lead and complete his brace.
The Nigerian then turned provider in the 59th minute, setting up Wijndal to score Ajax's third goal.
Davy Klaassen extended the advantage in the 67th minute with a close-range header after receiving a lofted pass from Kehrer.
Gloukh added a fifth in the 74th minute after weaving past several defenders before firing into the bottom corner.
Substitute Marcos Leonardo completed the rout in the 82nd minute, lifting the ball over goalkeeper Nordin Bakker before heading home to make it 6-1.
The victory strengthened Ajax's position in the Conference League, while Midtjylland were left to reflect on a difficult night after their numerical disadvantage proved costly.
Arokodare was named Flashscore's Man of the Match after scoring twice and providing an assist.
Result: FC Midtjylland 1-6 Ajax
Goals:
• Midtjylland: Friday Etim 28'
• Ajax: Tolu Arokodare 9', 52', Owen Wijndal 59', Davy Klaassen 67', Oscar Gloukh 74', Marcos Leonardo 82'
Red card:
• Midtjylland: Kjell Wätjen 43' (second yellow)