Monday's win was the Bergamo club's fourth consecutive home victory and lifts them into fifth spot, a point behind Fiorentina.
Dutch striker Teun Koopmeiners opening the scoring from the penalty spot after eight minutes.
Ederson doubled Atalanta's lead five minutes later with a neat half-volley, before Charles De Ketelaere added a third 60 seconds later when his left-foot shot crashed in off the underside of the bar.
Frosinone tighted things up after that and it took until the 83rd minute for substitute Davide Zappacosta to score the fourth after a quick counter-attack.
Emil Holm rounded out a comprehensive victory in the 90th minute.
The defeat - the fourth in a row in which Frosinone have conceded three goals or more - heaped more pressure on coach Eusebio Di Francesco.
His side have taken just one point from a possible 18 since the end of November and are one of only three Serie A teams still without an away win.
They lie 15th in the league, two points above the relegation zone.
Another club threatened with the drop, Empoli, have made their second coaching change of the season by sacking Aurelio Andreazzoli and replacing him with Davide Nicola.
The move came two days after second-from-bottom Empoli lost 2-1 at Hellas Verona, another club in the drop zone.
The 70-year-old Andreazzoli had signed a one-year contract in September to replace Paolo Zanetti.
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