Prueba esto:
$rows = mysql_query("SELECT `name`, `gender` FROM TABLE");
while ($row = mysql_fetch_assoc($rows)) {
if($row['gender'] == 1) {
$row['gender'] = 'Male';
} else {
$row['gender'] = 'Female';
}
// Or ternary condition
// $row['gender'] = ($row['gender'] == 1 ? 'Male' : 'Female');
fputcsv($output, $row);
}