NOTE: Potentially outdated. ECMAScript 2017 includes String.prototype.padStart.

You'll have to convert the number to a string since numbers don't make sense with leading zeros. Something like this:

function pad(num, size) {
    num = num.toString();
    while (num.length < size) num = "0" + num;
    return num;
}

Or, if you know you'd never be using more than X number of zeros, this might be better. This assumes you'd never want more than 10 digits.

function pad(num, size) {
    var s = "000000000" + num;
    return s.substr(s.length-size);
}

If you care about negative numbers you'll have to strip the - and re-add it.

function pad(toPad, padChar, length){
    return (String(toPad).length < length)
        ? new Array(length - String(toPad).length + 1).join(padChar) + String(toPad)
        : toPad;
}

pad(5, 0, 6) = 000005

pad('10', 0, 2) = 10 // don't pad if not necessary

pad('S', 'O', 2) = SO

...etc.

Cheers