Without seeing your code, it's hard to answer other than a stab in the dark. I would guess that the string you're passing to encodeURIComponent(), which is the correct method to use, is coming from the result of accessing the innerHTML property. The solution is to get the innerText/textContent property value instead:
var str,
el = document.getElementById("myUrl");
if ("textContent" in el)
str = encodeURIComponent(el.textContent);
else
str = encodeURIComponent(el.innerText);
If that isn't the case, you can use the replace() method to replace the HTML entity:
encodeURIComponent(str.replace(/&/g, "&"));
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