Preheat the oven to 350 degrees F. Line 2 baking sheets with parchment paper.
Whisk the flour, oats, flaxseed, baking soda, salt and cinnamon in a bowl.
Beat the butter, granulated sugar and brown sugar in a large bowl with a mixer on medium-high speed until fluffy, about 4 minutes. Beat in the eggs one at a time, beating well after each addition. Beat in the vanilla. Reduce the mixer speed to low; add the flour mixture and beat until just combined, scraping down the bowl as needed. Stir in the chocolate chips.
Drop heaping tablespoonfuls of dough onto the prepared baking sheets, about 2 inches apart. Bake until golden brown, 10 to 12 minutes. Let the cookies cool 3 minutes on the baking sheets, then transfer to racks to cool completely.