An election official said Ms Stein filed the request about an hour-and-a-half before a 5pm Friday deadline.
The Wisconsin Elections Commission said it is “preparing to move forward with a statewide recount of votes for President of the United States”.
The Green Party has been raising money to pay for votes to be recounted in Wisconsin, Michigan and Pennsylvania; crucial swing states during the election and all won by Donald Trump.
Although there is no evidence of election tampering in those states, Ms Stein, who stood as the party’s candidate in the election, has cited “anomalies” as grounds to mount a challenge in the three so-called Rust Belt states.
The deadlines for filing in Pennsylvania and Michigan are Monday and Wednesday of next week.
Green Party spokesman George Martin said: “There’s no smoking gun here, but we’re saying the American public needs to have it investigated to make sure our votes count.
“We’re doing this to ensure the integrity of our system.”
Donald Trump won Wisconsin, which was worth 10 electoral college votes, with 1,409,467 popular votes (47.9% of the total).
Hillary Clinton came second with 1,382,210 votes (46.9%) and Ms Stein polled 30,980 votes (1.1%).
Wisconsin is legally required to recount votes at a candidate’s request providing he or she can meet the costs, which election officials estimate to be up to $1m (£800,735).
The Green Party has so far raised $5.2m (£4,163,820).