  We address the challenge of incorporating encoded quantum memories into an
exact secret key rate analysis for small and intermediate-scale quantum
repeaters. To this end, we introduce the check matrix model and quantify the
resilience of stabilizer codes of up to eleven qubits against Pauli noise,
obtaining analytical expressions for effective logical error probabilities.
Generally, we find that the five-qubit and Steane codes either outperform more
complex, larger codes in the experimentally relevant parameter regimes or have
a lower resource overhead. Subsequently, we apply our results to calculate
lower bounds on the asymptotic secret key rate in memory-corrected quantum
repeaters when using the five-qubit or Steane codes on the memory qubits. The
five-qubit code drastically increases the effective memory coherence time,
reducing a phase flip probability of $1\%$ to $0.001\%$ when employing an error
syndrome identification adapted to the quantum noise channel. Furthermore, it
mitigates the impact of faulty Bell state measurements and imperfect state
preparation, lowering the minimally required depolarization parameter for
non-zero secret key rates in an eight-segment repeater from $98.4\%$ to
$96.4\%$. As a result, the memory-corrected quantum repeater can often generate
secret keys in experimental parameter regimes where the unencoded repeater
fails to produce a secret key. In an eight-segment repeater, one can even
achieve non-vanishing secret key rates up to distances of 2000 km for memory
coherence times of $t_c = 10$ s or less using multiplexing. Assuming a
zero-distance link-coupling efficiency $p_0 = 0.7$, a depolarization parameter
$\mu = 0.99$, $t_c = 10$ s, and an 800 km total repeater length, we obtain a
secret key rate of 4.85 Hz, beating both the unencoded repeater that provides
1.25 Hz and ideal twin-field quantum key distribution with 0.71 Hz at GHz clock
rates.
