Masakit ang tuhod ko pagkatapos kong tumakbo nang matagal kahapon.

Filipino very often uses predicate-first word order.

So in Masakit ang tuhod ko:

• Masakit = the predicate (painful / hurts / sore)
• ang tuhod ko = the topic or focused noun phrase (my knee)

This is a very normal structure in Filipino.
A more literal breakdown is something like:

• Masakit = hurts / is painful
• ang tuhod ko = my knee

So the sentence is not “backwards” in Filipino; it is following a common Filipino pattern.

Ang is a marker, not just the English word the.

In this sentence, ang marks tuhod ko as the topic of the sentence. It tells you which noun phrase the predicate is about.

So:

• ang tuhod ko = my knee as the topic

This is why ang is there even though English would not need a separate word for that function.

In Filipino, short possessive pronouns like ko usually come after the noun.

So:

• tuhod ko = my knee
• bahay ko = my house
• kaibigan ko = my friend

Here, ko means my.

This is a very common pattern:

• noun + ko = my + noun
• noun + mo = your + noun
• noun + niya = his/her + noun

Here, kong is understood as I, not my.

This is one of the things that can confuse learners, because ko can have different roles depending on the structure.

In:

• tuhod ko = my knee → ko is possessive
• pagkatapos kong tumakbo = after I ran → ko refers to the doer of tumakbo

So the same form ko can mean:

• my in a noun phrase
• I / me in certain grammatical constructions

In kong, the -ng is a linker attached to ko before the following word:

• ko + ng → kong

So:

• pagkatapos kong tumakbo = after I ran

The -ng in kong is a linker. Filipino often uses linkers to connect words smoothly inside a phrase.

Here it links ko and tumakbo in the clause after pagkatapos:

• pagkatapos ko-ng tumakbo
• written as pagkatapos kong tumakbo

You do not need to translate the linker directly into English. Its job is grammatical, not lexical.

A good way to think about it is:

• pagkatapos kong tumakbo = a natural Filipino way to say after I ran

It is better to think of tumakbo as showing completed aspect, not simple tense in the same way English does.

• tumakbo comes from takbo (run)
• the -um- verb form here gives tumakbo

In many contexts, tumakbo is understood as ran or has run, depending on the sentence.

In this sentence, it is clearly interpreted as a past completed action because of:

• pagkatapos = after
• kahapon = yesterday

So here:

• tumakbo = ran

Here, nang introduces an adverbial expression modifying the verb tumakbo.

• nang matagal = for a long time

This tells us how long the running lasted.

A helpful rule for learners is:

• ng often marks a non-topic noun
• nang is often used in adverbial expressions, especially with manner or duration

So in this sentence, nang matagal is the standard form.

Note: In casual writing, some native speakers mix up ng and nang, but for careful standard writing, nang matagal is appropriate here.

Matagal means long in duration.

So:

• nang matagal = for a long time

It does not mean physically long, like a long stick or a long road.
It means the action lasted a long time.

Examples:

• Naghintay ako nang matagal. = I waited for a long time.
• Tumakbo siya nang matagal. = He/She ran for a long time.

Time expressions in Filipino are fairly flexible in position.

So kahapon can often appear:

• at the beginning
• in the middle
• at the end

In this sentence, putting kahapon at the end is natural and makes it sound like it modifies the running event:

• pagkatapos kong tumakbo nang matagal kahapon
  = after I ran for a long time yesterday

A different but still natural arrangement would be:

• Pagkatapos kong tumakbo nang matagal kahapon, masakit ang tuhod ko.

So the end position is not strange; it is just one normal way to place the time word.

It is often described as an adjective, but in sentences like this it functions as the predicate, so in English it may be translated like a verb.

So:

• masakit literally has the sense painful / sore
• Masakit ang tuhod ko is naturally translated as My knee hurts or My knee is sore

This is very common in Filipino. Words that look adjective-like can serve directly as the main predicate of a sentence.

That is why:

• Masakit ang tuhod ko is completely normal even though English prefers the verb hurts.

Yes. Filipino allows quite a bit of flexibility in word order, especially when the markers already show the relationships between parts.

For example, this is also natural:

• Pagkatapos kong tumakbo nang matagal kahapon, masakit ang tuhod ko.

This puts the after clause first.

The original version:

• Masakit ang tuhod ko pagkatapos kong tumakbo nang matagal kahapon.

puts the main statement first:

• My knee hurts

Then it adds the circumstance:

• after I ran for a long time yesterday

Both are natural, but the emphasis feels slightly different depending on what comes first.