Today there is a clear gap between both. But what about before the 40s?
The biggest economic difference between the north and south before the Japanese colonial period (i.e., Joseon and earlier) is that the south is better for agriculture, and the north has more mineral resources.
The majority of wet-field rice cultivation was in the south. The longer growing season also allowed double-cropping (growing a crop of rice in a wet paddy, followed by a dry-field crop of barley was common). It was more difficult to grow rice and barley in the north, and millet and buckwheat were important crops in the north (they were also grown in the south, but more as an anti-famine crop in case other crops failed, rather than staples). The key result of this was that the population density in the south was much higher. This didn't necessarily mean that the average southern Korean was better off - most Koreans, both north and south, were famers living at close to subsistence level. The more productive land in the south simply meant that families could survive on less land. New crops from the Americas, in particular the potato, helped the north. The south also got new crops, such as the sweet potato and maize, so this didn't result in too much difference.
Under Japanese colonial rule, the economic position of poor farmers (i.e., most of the population) became worse. Much of the land passed to Japanese owners, and rents/taxes were higher than before. Rice consumption in Korea went down, with farmers eating more barley and millet (and Korean rice being exported to Japan).
The dominance of the north in mining and related industries goes back to at least the Three Kingdoms Period. This wouldn't have had much effect on most people, but of course affected farmers who had to provide compulsory labour for mines, and free miners (who were often ex-farmers who had lost their land and knew about mining from have provided such compulsory labour). As Korea industrialised during the Japanese colonial period, it resulted in a much bugger impact: most Korean heavy industry developed in the north. When Korea was divided, about 80% of heavy industry was in the north, while most agriculture was in the south (which also had a larger population). Other industries, like textiles, were much more evenly divided, with about 30% in the north and 70% in the south, which is close to the proportion of northern and southern populations (about 9 million and 16 million when Korea was divided).
Thus, when Korea was divided, the big differences between north and south were the industrialisation of the north and the higher population of the south.
The Korean War wrecked the economies of both the north and the south, leaving both Koreas with little in the way of heavy industry. North and South Korea were similar economically at the end of the war, both with very low GDP per capita:
(while the North Korean GDP per capita is shown as lower during 1950-1970, other estimates put the GPD per capita of the two Koreas as equal in this period, or the North Korean GDP per capita a little higher). It was only during the Park Chung-hee dictatorship that the South Korean economic recovery took off, resulting in South Korea's economy pulling ahead in about 1970-1975, and then growing quickly.
North Korea attempted a similar recovery, beginning at about the same time (1961). However, before the North Korean "recovery" could succeed, support from the Soviet Union fell, and the North Korean economy failed to grow. Poor economic management and North Korea defaulting on most of its international loand contributed to the failure to grow. Also, supporting armed forces approximately equal to those of the UK, France, and Germany combined, with a population of only 1/9 of those countries, and a GDP about 250 times smaller, must have limited growth.
Further reading:
For the Joseon period economy, see