Joe Root's record-equalling 33rd Test century had set the stage for England to build a commanding position after a challenging first day.
Resuming at 74 not out, Atkinson reached his maiden Test century with a drive past mid-on just before lunch. His innings included 14 fours and four sixes, ending at 118 when Asitha Fernando dismissed him. Fernando then completed his five-wicket haul by removing Olly Stone, wrapping up England's innings at 427 all out.
Sri Lanka's hopes of an early breakthrough were dashed as England delivered a superb team bowling performance. Chris Woakes and Stone quickly removed Dimuth Karunaratne and Pathum Nissanka within five balls, leaving Sri Lanka struggling at 35-3 by the end of the 10th over. The middle order offered little resistance.
Matthew Potts bowled Angelo Matthews and Dhananjaya de Silva in the 21st over, while Woakes, Stone, and Atkinson also took additional wickets as Sri Lanka collapsed. Kamindu Mendis provided some respite with a steady knock of 74 off 120 balls but edged Atkinson's delivery to Woakes for the final wicket.
Atkinson's brilliant 118 off 115 balls could be decisive in this Test, allowing England to build a strong lead despite limited support from the lower order. His previous best red-ball score was 21 not out against West Indies at Trent Bridge in July.
England avoided any drama when they batted for seven overs before stumps. Ben Duckett (15) and Ollie Pope (2) will resume on Saturday, aiming to extend their significant lead further.
The tourists' middle order failed to provide much-needed support as wickets fell regularly. Potts sent stumps flying to dismiss Angelo Matthews and Dhananjaya de Silva in quick succession during the 21st over. Woakes, Stone, and Atkinson also contributed to Sri Lanka's downfall.
Mendis' knock brought some relief for Sri Lanka but couldn't match his century from the first Test at Old Trafford. He eventually fell to Atkinson's delivery, caught by Woakes.
England ended their innings at 427 all out after Fernando claimed his fifth wicket by dismissing Stone. Despite this effort from Fernando, Sri Lanka struggled throughout their innings.
The day's play concluded with England in a dominant position, ready to build on their lead when play resumes on Saturday. Duckett and Pope will look to solidify their advantage further.