My 12 year old son runs a 20 minute 5k, but is not happy with his 16.88 100m. How can he improve on his speed without losing his endurance?

Mick Grant & John Molvar

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Speed development and endurance both take time. A simple workout you can add from time to time, as pure speed development, is something like 6 x 40 meter sprints. Use about a 20 meter acceleration and a 20 meter deceleration for a total of about 80 meters. He will sprint all out for 40 meters. Make sure he has a good warm up.
Be patient and think long term improvement.