This is pretty easy:
<field id="custom_file_upload"
translate="label"
type="file"
sortOrder="6"
showInDefault="1"
showInWebsite="1"
>
<label>Logo</label>
<backend_model>Magento\Config\Model\Config\Backend\File</backend_model>
<upload_dir config="system" scope_info="1">logo</upload_dir>
</field>
Further reading