Whalley was released by Hyde in order to join Southport for the second time in January 2011. He made his debut the following Saturday in a 4–0 win over York City, scoring Southport's second and fourth goals. On 1 February, less than a week later, Whalley scored again in a 2–2 draw with Grimsby Town to take his record to three goals in two games, before being sent off for violent conduct on and later receiving a four match ban. On 26 February after missing the best-part of that month through his suspension, he returned, to start in a 2–1 loss to Bath City, but he was unable to score a goal. He followed this game up by scoring in his next two, netting in the 3–1 win over Histon and then by scoring Southport's only goal, in a 4–1 defeat to Eastbourne Borough. He finished March having scored four goals that month, after adding another two in the latter part, the first in a 4–2 defeat to the hands of Barrow and the other coming as-part of a 2–2 draw with Rushden & Diamonds.