Millie, who despite being a consistent performer this season failed to register her first win, moved ahead of Aditi Ashok (77) and Gurbani Singh (74).
The 16-year-old Millie, a semi-finalist in last year's Usha All India Amateur Championships, was a picture of consistency as she sank two birdies. Her lone mistake came on the par-4 15th, which she bogeyed.
Millie, lying third overnight, is now one-over 145 for two days and one shot ahead of Gurbani (72-74) and two ahead of Aditi.
Aditi had a tough second round with four bogeys, one double bogey and just one birdie, while Gurbani had two bogeys on 12th and 16th and no birdies in her 74.
Amandeep Drall (75-75) was a distant fourth at 150 and Gursimar Badwal (79-77) was fifth.
Millie also led Category A, where Gurbani was second behind and Vrishali Sinha (80-76) was third.
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In Category B, despite her disappointing second round, Aditi led the field at 147 with Amrita Anand (79-81) and Gurjot Badwal (81-79) tied second at 160.
Arushi Pandey (86-79) was leading Category C, ahead of Riya Ahuja and Dhrishthi Karumbaya, who were tied second.
In Category D, Tanishka Kumar maintained her top spot with rounds of 91 and 99, while Tiya Choudhary was lying second.
Last year's winner of the Usha Northern India Ladies golf, Vani Kapoor has since turned professional. Gurbani was second last time and would like to improve on that, while Aditi was third.