Why Your Knees Ache Late in Long Runs (And 4 the Quad Exercises Runners Actually Need)
- Marie Whitt
- Feb 9
- 5 min read
I was in big trouble.
Only half way down the mountain and my right knee is screaming at me.
(This was last week during ski week, just to be clear).
Don't worry, it all still relates to running and cantakerous knees.
Because for the past 2 years I've been religious about strength training like a runner 2-3x a week.
Specifically ALWAYS hitting leg day at least 1 time a week. If not 2.
And not skimping on the single leg work which would set my quads ablaze and make me question my life choices.
And here I am, wondering where all my hard work went.
Until I realized, I hadn't been able to do a strength workout like normal for about 2 weeks because of being sick with this winter season's plague.
Cool cool.
But the crazy part?
I knew I could hang on.
I knew I could tough it out flying down the mountain without injuring myself BECAUSE of all the deliberate work I'd done to fix my runner's knee for good.
I kept telling myself:
You don't lose fitness overnight.
You don't lose muscles strength or tendon stiffness in 2 weeks.
Your patellar tendon is talking right now because of the increased time under tension...
And you're still going to be able to run again when you get home.
And I could.
And I did.
I realize, as runners, we care much more about how our knees perform on the back half of our 20 milers rather than the second half of the mountain descent.
And we care much more about how they feel while running down hills mid race than we do walking across a parking lot with clunky ski boots on.
Same pain; different situation.
And as a result of last week's knee shenangians, it put me into problem solving mode of what exercises exactly would I use for myself?
So I wrote you a circuit that gets to the root cause of WHY your knee aches at the end of your long run and after a hill workout regardless of how many back squats you do.
Because you may be lifting heavy.
You may be strength training consistently.
But the exercises you do MATTER.
And HOW you do them matter.
So let's hop in.

Runner-Specific Quad and Glute Exercises for Knee Pain
Circuit:
see sets below // medium-heavy weights
Alternating Lunge Jump
3 X 6-12 jumps per leg
Single Leg Hip Thrust with High Knee
4 X 6 reps ea leg weight (heavy weight!)
Forward Walking Lunge with Single Weight Overhead
3 x 10 reps each leg (medium weight)
Single Leg Squat to Box
4 x8 reps ea leg (medium weight)
emphasis on 3 secs descent; 3 secs ascent
Why Back Squats Alone Don’t Fix Runner’s Knee
Alternating Lunge Jump
I need you to stop making excuses for skipping these...
THE REASON: please read between the lines: if your knees are currently flared up, then yes, of course wait to do these.
But if you're like me from 6 years ago who refused to do these because "they look hard", that's not gonna cut it.
Our knee pain as runners frequently comes from poor eccentric quad strength, lack of quad muscle endurance, and a not-very-strong patellar tendon. This particular exercise directly targets that cranky tendon that puts up a fight after your quad muscle has fatigued and checked out for the day.
Just becareful: Don't slam your knee into the ground. It's important to stop low to the ground in a deep yield position, as this is where maximum stretch and load occurs on the tendon, but if this movement feels too awkward for your brain, add a stutter step.
A stutter step is where you stop mid leg-scissor. As your front leg and back leg are sweeping to switch positions, there's a moment where they meet under you. Just pause the motion here. And continue the jump. I used this exact strategy for about 2 weeks before I could do the full jump without irritating my knee.
Single Leg Hip Thrust with High Knee
I know this can feel awkward, but hang with me.
THE PURPOSE: while your quads get either all the glory or all the blame for knee pain, it's still crucial to keep your glutes strong.
I love this version of a hip thrust because you can easily do it at home using a couch or a foot stool. And with it being single leg, you can stretch the use of your home gym weights a little further since single leg is automatucally harder than bilateral (two) legs, making your heavy weight a little lighter.
And yes, I like the opposite knee up in a high knee position for a little extra balance and core challenge; plus it puts you in a position that resembles your running stride, giving your body a preview of how and when it'll use this new strength.
Forward Walking Lunge with Single Weight Overhead
Here's the catch: this doesn't quite replace the good ol' basic walking lunge but...
TOP TIP: occasionally I like to use a heavy weight overhead to test my core. I realize however, that I can't go nearly as heavy as if I was carrying to dumbbells down my sides but...
I want you to play with this. I want you to feel your body and how your core has to fight to stay upright, supporting both your arm overhead, and the locomotion of your lower body. You'll automatically train your same-sided glute and quad to work together to create greater pelvic stability, improved core strength, while still challenging your single leg strength in a new way.
And sometimes, novel stimuli like this is a fun way to determine which side might be weaker and we can feel improvements faster.
Single Leg Squat to Box
This is where the magic happens.
THE SECRET: you cannot skip this one. This is the money shot. But the magic happens when you slow down. That's why I've emphasized the need to focus on lowering yourself down to your bench, chair, or box for 3 secs and then taking 3 seconds to travel back up. (If you're a little faster, it's ok).
But it's this particular tempo rep scheme that DIRECTLY targets your tendon. When we move faster (1 sec up/ 1 sec down), we provide a hypertrophy or muscle growth stimuli more to our quads and tendons. But with increased time under tension, (3 secs down/ 3 secs up) we send that "get stronger" message to our tendon instead.
Don't feel bad if you need to start with body weight. I care more about you controlling the motion, with the right rep scheme, and NO plopping onto the bench, then I do about how heavy you can go at first.
WRAPPING UP
If there’s one thing I want you to take away from this, it’s this:
It's a sign.
Your quads and patellar tendon don’t have the endurance and control to keep up with the demands of the fatigue that set in on the back half of long runs or downhill miles.
And as a runner, you deserve more than the generic leg day exercises the internet tries to feed you.
You also don't to stop running every time your knee throws a tempter tantrum.
That's your signal to work smarter, not harder and dive into runner-specific strength:
done with intention
focused on single-leg work
with a controlled tempos
with exercises that load the knee the way running actually does, especially as fatigue sets in.
So be patient.
Start with where you are and what you can do.
Slow your reps down.
And your knees will thank you.
Dare to Train Differently,
Marie Whitt, PT, DPT //@dr.whitt.fit



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