We present the results of a semicoherent search for continuous gravitational waves from the low-mass X-ray binary Scorpius X-1, using data from the first Advanced LIGO observing run. The search method uses details of the modeled, parametrized continuous signal to combine coherently data separated by less than a specified coherence time, which can be adjusted to trade off sensitivity against computational cost. A search was conducted over the frequency range 25– ##IMG## [http://ej.iop.org/images/0004-637X/847/1/47/apjaa86f0ieqn1.gif] $2000,mathrmHz$ , spanning the current observationally constrained range of binary orbital parameters. No significant detection candidates were found, and frequency-dependent upper limits were set using a combination of sensitivity estimates and simulated signal injections. The most stringent upper limit was set at ##IMG## [http://ej.iop.org/images/0004-637X/847/1/47/apjaa86f0ieqn2.gif] $175,mathrmHz$ , with comparable limits set across the most sensitive frequency range from 100 to ##IMG## [http://ej.iop.org/images/0004-637X/847/1/47/apjaa86f0ieqn3.gif] $200,mathrmHz$ . At this frequency, the 95% upper limit on the signal amplitude h 0 is ##IMG## [http://ej.iop.org/images/0004-637X/847/1/47/apjaa86f0ieqn4.gif] $2.3times 10^-25$ marginalized over the unknown inclination angle of the neutron star’s spin, and ##IMG## [http://ej.iop.org/images/0004-637X/847/1/47/apjaa86f0ieqn5.gif] $8.0times 10^-26$ assuming the best orientation (which results in circularly polarized gravitational waves). These limits are a factor of 3–4 stronger than those set by other analyses of the same data, and a factor of ∼7 stronger than the best upper limits set using data from Initial LIGO science runs. In the vicinity of ##IMG## [http://ej.iop.org/images/0004-637X/847/1/47/apjaa86f0ieqn6.gif] $100,mathrmHz$ , the limits are a factor of between 1.2 and 3.5 above the predictions of the torque balance model, depending on the inclination angle; if the most likely inclination angle of 44° is assumed, they are within a factor of 1.7.