Top projects at the US space agency would continue, including developing a new spaceship to send astronauts to the International Space Station, working toward an asteroid rendezvous and the 2018 launch of the James Webb Space Telescope.
Obama's plan, which stands little chance of being enacted by a deadlocked Congress and Senate that have already passed their own budgets, allows for $17.7 billion for NASA, a decrease of 0.3 percent, or $50 million below 2012.
Much of that decline comes from moving education programs for science, technology, engineering, and mathematics, known by the acronym STEM, out of NASA as part of a major reshuffle.
Ninety STEM programs across 11 different agencies -- all worth a total of $180 million -- are being funnelled into the Department of Education, in what Obama's budget described as "the single biggest consolidation proposed this year."
This "reorganization" aims to "improve the delivery, impact, and visibility of STEM efforts," the budget document said.
Both job and budget cuts were foreseen for the Environmental Protection Agency, which would receive $8.2 billion, or a 3.5 percent cut below the 2012 enacted level.
The decrease in $296 million at the EPA would be achieved, in part, through "consolidating positions and restructuring the workforce to ensure the Agency has the necessary skills for the current era of environmental protection," it said.
Meanwhile, funding would rise for the National Science Foundation, with an increase of $593 million over 2012 to an annual $7.6 billion budget.
The plan "maintains the President's commitment to increase funding for key basic research agencies, including a robust 8.4 percent increase over the 2012 enacted level for the National Science Foundation," it said.
Another budget boost was included for Health and Human Services as Obama's healthcare reform plan continues to be implemented in the coming years.
The $80.1 billion he called for at HHS represents $3.9 billion above the 2012 enacted level.
The $31 billion for the National Institutes of Health was unchanged, but more cash would go to Alzheimer's research, HIV prevention and treatment, family planning, mental health services and gun violence prevention, the budget said.
The Department of Energy would also get an eight percent boost over 2012, with $28.4 billion in discretionary funds.
The DOE rise would "position the United States to compete as a world leader in clean energy" as well as respond to climate change and "modernize the nuclear weapons stockpile and infrastructure," it said.
The plan would eliminate $4 billion in "annual unwarranted and unnecessary subsidies to the oil, gas, and coal industries," it said.
Other savings would be achieved through some modifications to Medicare, such as aligning drug payment policies for people over 65 with those for low-income people receiving Medicaid, saving $123 billion over the next 10 years, it said.