The prolific striker then went on to complete back-to-back hat-tricks following the three goals that he struck against Dagenham and Redbridge in the FA Cup last weekend.
City's first chance arrived on five minutes when skipper Matty Oakley headed Kerrea Gilbert's cross narrowly wide.
But there was to be no reprieve for Southend on six minutes when Fryatt took Oakley's pass in his stride and cut inside Adam Barrett before he beat the keeper with a low angled drive from 14 yards.
Southend almost equalised with what was to be their best chance of the game on 15 minutes when Simon Francis crossed the near post where Alex Revell fired just over from close range.
But it was City who continued to dominate with Lloyd Dyer spurning a chance on 25 minutes when he fired a free-kick straight at the keeper after Peter Clarke had fouled Steven Howard on the edge of the area.
Fryatt was denied what seemed a certain second goal on 35 minutes when Barrett dived in to block the striker's shot from six yards.
After the break, Leicester were relieved to clear their lines when David Martin spilled a Kevin Betsy drive before Fryatt failed to connect with Gilbert's far-post cross.
Steve Mildenhall came to Southend's rescue when he used his feet to keep out a fierce shot from substitute Mark Davies before Fryatt drove narrowly over from 20 yards.
But there was no denying Fryatt on 76 minutes when he latched onto a Howard flick-on and left Barrett on the seat of his pants before beating Mildenhall comprehensively from 14 yards.
And Fryatt had his hat-trick on 80 minutes when he confidently stroked home a penalty after Clarke had handled inside the area.
Five minutes from the end, Fryatt made way for Paul Dickov to a standing ovation before Leicester went on to complete their sixth home win on the trot.