Yes there is. ACF stores fields on user forms in the usermeta table.
The difficulty is that checkbox fields are arrays stored as serialized data. In order to do a user query you would need to use the “LIKE” compare method in the meta_query for the user query.
something like
'meta_query' => array(
array(
'key' => 'my_field',
'value' => 'my_value',
'compare' => 'LIKE'
)
)
if you’re looking for more than one value then you’d need to look for each value with and ‘AND’ or ‘OR’ for the relation value, depending on what you want returned.
https://codex.wordpress.org/Class_Reference/WP_User_Query
