When working interactively with the MySQL client, you receive feedback of the time the query took to complete to a granularity of 10 ms.

Enabling profiling is a simple way to get more a more accurate timing of running queries. In the following example you can see the time the kernel took to run an explain, the query, and alter, and repeat explain and query.

mysql> set profiling=1;
mysql> EXPLAIN SELECT ...
mysql> SELECT ...
mysql> ALTER ...
mysql> show profiles;
+----------+------------+-------------------------
| Query_ID | Duration   | Query
+----------+------------+-------------------------
|        1 | 0.00036500 | EXPLAIN SELECT sbvi.id a
|        2 | 0.00432700 | SELECT sbvi.id as sbvi_i
|        3 | 2.83206100 | alter table sbvi drop in
|        4 | 0.00047500 | explain SELECT sbvi.id a
|        5 | 0.00367100 | SELECT sbvi.id as sbvi_i
+----------+------------+-------------------------

More information at Show Profiles documentation page.