The problem is that you are applying ceil to the outer expression. Try to rewrite it as:

$charges = 9;
$cost = 100;

echo ($cost + ceil($cost * $charges / 100)) * 100;

This outputs 10900 as expected.

UPDATE

As @cars10m suggested, simplifying the expression does help:

echo ceil($cost * 100  + $cost * $charges);

UPDATE 2

You can also use BCMath library to do precise math:

bcscale(6);
echo ceil(bcadd(bcmul($cost, 100), bcmul($cost, $charges)));

you have 3 possibility : round(), floor(), ceil()

for you :

$step = 2; // number of step 3th digit
$nbr = round(2.333333333 * $step, 1) / $step; // 2.35

$step = 4; // number of step on 3th digit
$nbr = round(2.333333333 * $step, 1) / $step; // 2.325

round

<?php
echo round(3.4);         // 3
echo round(3.5);         // 4
echo round(3.6);         // 4
echo round(3.6, 0);      // 4
    echo round(1.95583, 2);  // 1.96
echo round(1241757, -3); // 1242000
echo round(5.045, 2);    // 5.05
echo round(5.055, 2);    // 5.06
?>

floor

<?php
echo floor(4.3);   // 4
echo floor(9.999); // 9
echo floor(-3.14); // -4
?>

ceil

<?php
echo ceil(4.3);    // 5
echo ceil(9.999);  // 10
echo ceil(-3.14);  // -3
?>