Why does modulus operator return fractional number in javascript?

Because JavaScript uses floating point math which can lead to rounding errors.

If you need an exact result with two decimal places, multiply your numbers with 100 before the operation and then divide again afterwards:

var result = ( 4990 % 10 ) / 100;

Round if necessary.

Javascript's Number is using "IEEE double-precision" to store the values. They are incapable of storing all decimal numbers exactly. The result is not zero because of round-off error when converting the decimal number to binary.

49.90 = 49.89999999999999857891452848...
 0.10 =  0.10000000000000000555111512...

Thus floor(49.90 / 0.10) is only 498, and the remainder will be 0.09999....

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It seems that you are using numbers to store amount of dollars. Don't do this, as floating point operations propagate and amplify the round-off error. Store the number as amount of cents instead. Integer can be represented exactly, and 4990 % 10 will return 0.