Toggle Checkbox using JavaScript

How about using an operator, that is defined to toggle booleans using 1 as second operand?

inputs[i].checked ^= 1;

This uses the XOR Compound assigment operator, and it toggles booleans because ¬A ≡ A ^ 1.

It also doesn't require looking up inputs[i] a second time.

2020 update: You can also eliminate the for loop and all those vars by using the forEach function to iterate over the checkboxes, reducing your function body to:

document.querySelectorAll('input[type="checkbox"]').forEach(e => e.checked ^= 1);

It can be easier:

inputs[i].checked = !inputs[i].checked;

Single equals is assignment, double/triple equals is for equality. You need to use double or triple equals in your if/else block.

    if(inputs[i].checked == false) {
        inputs[i].checked = true; 
    }
    else {
        if(inputs[i].checked == true) {
            inputs[i].checked = false; 
         }   
    }