To solve this problem, let's examine each option step by step:

Option A: $a^{2}+a^{4}$

- This option suggests adding two powers of $a$. However, without a common exponent, these terms cannot be combined through addition. Therefore, $a^{2}+a^{4} \neq a^{6}$.

Option B: $a^{2}\cdot a^{3}$

- When multiplying terms with the same base, we add their exponents according to the rule $a^{m} \cdot a^{n} = a^{m+n}$. Thus, $a^{2}\cdot a^{3} = a^{2+3} = a^{5}$, not $a^{6}$.

Option C: $(-a^{2})^{3}$

- Raising a term to a power involves multiplying the exponent inside the parentheses by the outside exponent. For $(-a^{2})^{3}$, we get $(-1)^{3} \cdot a^{2\cdot3} = -a^{6}$, which is not equal to $a^{6}$ due to the negative sign.

Option D: $a^{8}\div a^{2}$

- When dividing terms with the same base, we subtract the exponent of the denominator from the exponent of the numerator according to the rule $a^{m} \div a^{n} = a^{m-n}$. Therefore, $a^{8}\div a^{2} = a^{8-2} = a^{6}$.

Given the examination above, the correct operation is found in Option D, where $a^{8}\div a^{2}=a^{6}$.

Thus, the correct answer is $\boxed{D}$.