Refresh a particular output panel in some specific interval of time in Salesforce Visualforce Page

Hello Piyush,

There is a remarkable attribute within <apex:actionPoller> component is "enabled". With the use of this attribute, you may achieve your requirement.

Visual Force Page - 

<apex:page controller="Referesh_A_Certain_At_Sertain_TimeCtrl">
<style>
.Processing{
position: fixed;
background: url('/img/loading32.gif');
background-repeat: no-repeat;
background-position: center;
width: 100%;
height: 100%;
z-index: 10004;
left: 0%;
top: 0%;
}
</style>
<apex:form >
<apex:actionStatus id="idStatus" startStyleClass="Processing" ></apex:actionStatus>
<apex:actionPoller action="{!increment}" rerender="count" interval="5" enabled="{!IF(count < 0,false,true)}" status="idStatus" />

<apex:outputPanel id="count">
{!IF(count < 0,false,true)}
{!count}
</apex:outputPanel>
</apex:form>
</apex:page>

Controller -

public class Referesh_A_Section_At_Certain_TimeCtrl{
public Decimal count {get; set;}
public Referesh_A_Section_At_Sertain_TimeCtrl(){
count = 0;
}
public void increment(){
count++;
}
}

Hope it helps