Parsing file using indexOf() method in Java

Instead of indexOf(), i would suggest StringTokenizer. basically you can split you String based on some separator (eg: ;)..

Example inside your while loop

        StringTokenizer st = new StringTokenizer(line,";");


        st.nextToken(); //Date
        st.nextToken(); //AM
        String email = st.nextToken();
        String values = st.nextToken();

        StringTokenizer st2 = new StringTokenizer(values," ");


        while (st2.hasMoreElements()) {
            String token = (String) st2.nextElement();
            if(token.startsWith("student=")){
                System.out.println(token.substring("student=".length()));
            }else if(token.startsWith("std=")){
                System.out.println(token.substring("std=".length()));
            }

        }

You don't need to use indexOf for everything. If you want to look at one character, you can use charAt() e.g. where you are checking for a '"'

I would use a method which extracts the value for a field to simplify the code.

As I stated in an earlier comment, I am surprised that the parsing is the bottleneck here. But if you wish to know other ways that you could do this, and just try them out and see which is the fastest, here are two more ideas that haven't been posted- using .split:

String[] arr1 = line.split(";");
String dateTime = arr1[0];
String ampm = arr1[1];
String email = arr1[2];
String[] arr2 = arr1[3].split(" ");
String student, std, marks, rollnumber;
student = std = marks = rollnumber = null;
for (String str : arr2) {
    String value = str.substring(str.indexOf("=") + 1);
    switch(str.charAt(2)) {
    case 'u': student = value; break;
    case 'd': std = value; break;
    case 'r': marks = value; break;
    case 'l': rollnumber = value; break;
    }
}

Or using a regex:

private static final Pattern PATTERN = Pattern.compile("([^;]+);([^;]+);([^;]+);student=([^ ]+) std=([^ ]+) marks=([^ ]+) rollnumber=([^ ]+)");

Matcher m = PATTERN.matcher(line);
m.find();
String dateTime = m.group(1);
String ampm = m.group(2);
String email = m.group(3);
String student = m.group(4);
String std = m.group(5);
String marks = m.group(6);
String rollnumber = m.group(7);